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Barium in PDB 4u87: Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)

Protein crystallography data

The structure of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group), PDB code: 4u87 was solved by D.R.Boer, J.A.Ruiz Maso, G.Del Solar, M.Coll, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.77 / 3.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.800, 85.800, 246.160, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 23.7

Other elements in 4u87:

The structure of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) also contains other interesting chemical elements:

Manganese (Mn) 3 atoms
Chlorine (Cl) 3 atoms

Barium Binding Sites:

The binding sites of Barium atom in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) (pdb code 4u87). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 9 binding sites of Barium where determined in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group), PDB code: 4u87:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Barium binding site 1 out of 9 in 4u87

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Barium binding site 1 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 1 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba302

b:0.4
occ:0.50
 O B:ASP129 2.9 0.6 1.0
O B:VAL132 3.3 75.9 1.0
OE1 B:GLU181 3.6 93.7 1.0
C B:ASP129 4.0 0.5 1.0
CG2 B:VAL132 4.4 75.7 1.0
C B:VAL132 4.5 75.5 1.0
CB B:ASP129 4.5 0.6 1.0
CA B:ASP129 4.6 0.9 1.0
CD B:GLU181 4.7 90.3 1.0
CD1 B:LEU178 4.9 82.3 1.0

Barium binding site 2 out of 9 in 4u87

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Barium binding site 2 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba303

b:0.3
occ:1.00
 OE1 B:GLU138 4.0 0.5 1.0
CD B:GLU138 4.9 0.9 1.0
OE2 B:GLU138 4.9 0.7 1.0

Barium binding site 3 out of 9 in 4u87

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Barium binding site 3 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba304

b:0.7
occ:0.50
 O B:ASP166 3.3 99.7 1.0
C B:ASP166 4.5 95.7 1.0

Barium binding site 4 out of 9 in 4u87

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Barium binding site 4 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba305

b:0.3
occ:0.50
 O B:GLU16 3.2 0.9 1.0
C B:GLU16 4.1 0.9 1.0
CA B:GLU16 4.7 0.9 1.0
O B:ILE18 4.8 0.6 1.0
O B:PRO15 4.8 0.5 1.0

Barium binding site 5 out of 9 in 4u87

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Barium binding site 5 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 5 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba302

b:0.1
occ:1.00
 O C:VAL132 3.1 93.2 1.0
O C:ASP129 3.2 0.5 1.0
C C:ASP129 4.1 0.4 1.0
C C:VAL132 4.2 90.9 1.0
OE1 C:GLU181 4.4 87.1 1.0
CB C:ASP129 4.4 0.5 1.0
CA C:ASP129 4.7 0.3 1.0
OE2 C:GLU181 4.8 85.7 1.0
CD C:GLU181 4.9 84.3 1.0

Barium binding site 6 out of 9 in 4u87

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Barium binding site 6 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 6 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba303

b:0.9
occ:0.50
 O C:THR133 3.4 0.4 1.0
OE2 C:GLU138 3.5 0.5 1.0
NZ B:LYS63 3.5 98.3 1.0
OE1 C:GLU138 3.8 0.1 1.0
CE B:LYS63 4.0 96.7 1.0
CD C:GLU138 4.0 0.1 1.0
C C:THR133 4.5 0.6 1.0
OE1 C:GLU94 4.6 99.4 1.0
CG1 C:VAL132 4.8 86.4 1.0
CD B:LYS63 4.9 93.0 1.0
O B:GLY30 4.9 0.8 1.0

Barium binding site 7 out of 9 in 4u87

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Barium binding site 7 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba304

b:92.9
occ:0.50
 O C:GLN49 3.0 0.6 1.0
O C:SER44 3.4 99.0 1.0
O C:ILE46 3.5 0.6 1.0
C C:GLN49 3.8 0.2 1.0
N C:GLN49 4.1 0.0 1.0
N C:LYS50 4.4 0.2 1.0
CA C:LYS50 4.5 0.9 1.0
CA C:GLN49 4.6 0.8 1.0
C C:SER44 4.6 96.4 1.0
C C:ILE46 4.6 1.0 1.0
N C:GLY48 4.7 99.3 1.0

Barium binding site 8 out of 9 in 4u87

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Barium binding site 8 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 8 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba305

b:0.9
occ:0.50
 O C:ASP166 3.2 0.2 1.0
C C:ASP166 4.4 0.2 1.0

Barium binding site 9 out of 9 in 4u87

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Barium binding site 9 out of 9 in the Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group)


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 9 of Crystal Structure of the Ba-Soaked C2 Crystal Form of PMV158 Replication Initiator Repb (P3221 Space Group) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ba306

b:0.7
occ:0.50
 O C:GLU16 3.5 0.0 1.0
C C:GLU16 4.6 0.0 1.0

Reference:

D.R.Boer, J.A.Ruiz-Maso, M.Rueda, M.V.Petoukhov, C.Machon, D.I.Svergun, M.Orozco, G.Del Solar, M.Coll. Conformational Plasticity of Repb, the Replication Initiator Protein of Promiscuous Streptococcal Plasmid PMV158. Sci Rep V. 6 20915 2016.
ISSN: ESSN 2045-2322
PubMed: 26875695
DOI: 10.1038/SREP20915
Page generated: Wed Jul 10 15:31:05 2024

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