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Barium in PDB 6jxm: Crystal Structure of PHI29 Prna Domain II

Protein crystallography data

The structure of Crystal Structure of PHI29 Prna Domain II, PDB code: 6jxm was solved by R.Cai, I.R.Price, F.Ding, F.Wu, T.Chen, Y.Zhang, G.Liu, P.J.Jardine, C.Lu, A.Ke, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 101.18 / 3.32
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 120.178, 120.178, 187.494, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.5

Other elements in 6jxm:

The structure of Crystal Structure of PHI29 Prna Domain II also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Barium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Barium atom in the Crystal Structure of PHI29 Prna Domain II (pdb code 6jxm). This binding sites where shown within 5.0 Angstroms radius around Barium atom.
In total 15 binding sites of Barium where determined in the Crystal Structure of PHI29 Prna Domain II, PDB code: 6jxm:
Jump to Barium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Barium binding site 1 out of 15 in 6jxm

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Barium binding site 1 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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 PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba108

b:0.6
occ:1.00
O4 B:U50 2.9 92.8 1.0
O6 B:G51 3.0 94.2 1.0
C6 B:G51 4.0 0.3 1.0
O6 B:G39 4.0 0.2 1.0
C4 B:U50 4.1 0.9 1.0
N1 B:G51 4.3 0.8 1.0
O6 B:G49 4.6 0.3 1.0
N3 B:U50 4.6 0.1 1.0
OP2 B:A38 4.8 87.8 1.0
OP2 B:A37 4.9 96.2 1.0

Barium binding site 2 out of 15 in 6jxm

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Barium binding site 2 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 2 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba109

b:0.5
occ:1.00
O6 B:G66 3.4 0.1 1.0
OP2 B:A22 4.0 0.7 1.0
C6 B:G66 4.5 0.4 1.0
O6 B:G65 4.7 0.3 1.0
OP1 B:A22 4.7 1.0 1.0
P B:A22 4.8 0.8 1.0
N1 B:G66 4.9 0.6 1.0

Barium binding site 3 out of 15 in 6jxm

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Barium binding site 3 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 3 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba110

b:0.7
occ:1.00
O4 B:U86 3.3 0.7 1.0
O6 B:G7 3.3 0.7 1.0
O6 B:G70 3.3 1.0 1.0
O6 B:G85 3.3 0.4 1.0
C6 B:G7 4.1 0.2 1.0
N7 B:G70 4.2 0.5 1.0
N4 B:C71 4.2 0.0 1.0
C6 B:G70 4.3 1.0 1.0
C4 B:U86 4.3 0.8 1.0
N3 B:U86 4.5 1.0 1.0
C6 B:G85 4.5 0.2 1.0
N7 B:G7 4.6 0.5 1.0
C5 B:G70 4.7 0.6 1.0
C5 B:G7 4.7 0.2 1.0
N4 B:C87 5.0 0.2 1.0

Barium binding site 4 out of 15 in 6jxm

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Barium binding site 4 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 4 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba111

b:1.0
occ:1.00
O4 B:U76 3.2 0.6 1.0
C4 B:U76 4.1 0.7 1.0
BA B:BA113 4.3 0.6 1.0
C5 B:U76 4.4 0.8 1.0
OP1 B:G78 4.9 0.7 1.0

Barium binding site 5 out of 15 in 6jxm

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Barium binding site 5 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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 PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba112

b:0.3
occ:1.00
O6 B:G74 3.3 0.3 1.0
O2' B:A79 3.4 0.8 1.0
O6 B:G73 3.6 0.2 1.0
N7 B:G73 4.0 0.7 1.0
N7 B:G74 4.1 1.0 1.0
C6 B:G74 4.2 98.3 1.0
C6 B:G73 4.3 0.9 1.0
N4 B:C82 4.4 0.1 1.0
C5 B:G73 4.4 0.6 1.0
C5 B:G74 4.5 94.5 1.0
C2' B:A79 4.6 0.9 1.0
OP2 B:U81 4.8 0.3 1.0

Barium binding site 6 out of 15 in 6jxm

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Barium binding site 6 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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 PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba113

b:0.6
occ:1.00
OP2 B:A79 3.0 0.7 1.0
O4 B:U76 3.1 0.6 1.0
O4 B:U75 3.2 0.3 1.0
OP1 B:A79 3.7 0.2 1.0
P B:A79 3.8 0.1 1.0
C4 B:U76 4.2 0.7 1.0
BA B:BA111 4.3 1.0 1.0
C4 B:U75 4.3 0.0 1.0
N3 B:U76 4.5 0.1 1.0
O5' B:A79 4.7 0.2 1.0
C5 B:U75 4.8 0.2 1.0

Barium binding site 7 out of 15 in 6jxm

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Barium binding site 7 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 7 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba114

b:0.4
occ:1.00
N7 B:G17 3.6 0.5 1.0
O6 B:G17 4.0 0.0 1.0
O6 B:G78 4.0 0.2 1.0
C5 B:G17 4.5 0.3 1.0
C6 B:G17 4.6 0.4 1.0
O2' B:U76 4.6 0.6 1.0
C8 B:G17 4.6 1.0 1.0

Barium binding site 8 out of 15 in 6jxm

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Barium binding site 8 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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 PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba115

b:0.1
occ:1.00
OP2 B:A9 2.8 0.5 1.0
OP1 B:A9 3.3 0.4 1.0
P B:A9 3.5 0.4 1.0
OP1 B:U8 3.7 0.2 1.0
OP2 B:U11 3.8 0.9 1.0
OP2 B:U8 4.0 0.8 1.0
BA B:BA120 4.1 0.4 1.0
P B:U8 4.3 0.9 1.0
O3' B:U8 4.5 1.0 1.0
OP2 B:U12 4.5 0.8 1.0
N4 B:C13 4.6 0.9 1.0
C3' B:U8 4.6 0.7 1.0
C5 B:C13 4.8 0.4 1.0
O5' B:A9 4.8 0.4 1.0
O5' B:U8 4.8 0.0 1.0
C5 B:U12 4.9 0.3 1.0

Barium binding site 9 out of 15 in 6jxm

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Barium binding site 9 out of 15 in the Crystal Structure of PHI29 Prna Domain II


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 PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba116

b:0.8
occ:1.00
OP1 B:A44 3.4 0.1 1.0
P B:A44 4.7 0.2 1.0
C3' B:U43 5.0 0.7 1.0

Barium binding site 10 out of 15 in 6jxm

Go back to Barium Binding Sites List in 6jxm
Barium binding site 10 out of 15 in the Crystal Structure of PHI29 Prna Domain II


Mono view


Stereo pair view

A full contact list of Barium with other atoms in the Ba binding site number 10 of Crystal Structure of PHI29 Prna Domain II within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ba117

b:1.0
occ:1.00
O6 B:G52 3.6 0.5 1.0
N7 B:G36 3.9 0.9 1.0
O6 B:G36 4.4 0.6 1.0
C5 B:G36 4.6 0.8 1.0
N7 B:G51 4.6 0.1 1.0
O6 B:G51 4.7 94.2 1.0
C8 B:G36 4.7 0.7 1.0
C6 B:G36 4.8 0.2 1.0
C6 B:G52 4.8 0.5 1.0

Reference:

R.Cai, I.R.Price, F.Ding, F.Wu, T.Chen, Y.Zhang, G.Liu, P.J.Jardine, C.Lu, A.Ke. Atp/Adp Modulates GP16-Prna Conformational Change in the PHI29 Dna Packaging Motor. Nucleic Acids Res. V. 47 9818 2019.
ISSN: ESSN 1362-4962
PubMed: 31396619
DOI: 10.1093/NAR/GKZ692
Page generated: Wed Jul 10 15:54:54 2024

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