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Sodium in PDB 2xjh: Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B

Enzymatic activity of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B

All present enzymatic activity of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B:
1.15.1.1;

Protein crystallography data

The structure of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B, PDB code: 2xjh was solved by A.El-Ghazouani, A.Basle, S.J.Firbank, C.W.Knapp, J.Gray, D.W.Graham, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 0.92
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 29.475, 29.475, 29.480, 90.00, 90.00, 90.00
R / Rfree (%) 12.5 / 14.1

Other elements in 2xjh:

The structure of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B also contains other interesting chemical elements:

Copper (Cu) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B (pdb code 2xjh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B, PDB code: 2xjh:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 2xjh

Go back to Sodium Binding Sites List in 2xjh
Sodium binding site 1 out of 3 in the Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1002

b:9.2
occ:1.00
 O A:BB91 2.4 6.8 1.0
C A:BB91 3.3 6.0 1.0
O2 A:COI0 3.5 6.5 1.0
CA A:BB91 4.7 5.0 1.0
C1 A:COI0 4.9 6.7 1.0

Sodium binding site 2 out of 3 in 2xjh

Go back to Sodium Binding Sites List in 2xjh
Sodium binding site 2 out of 3 in the Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1003

b:8.8
occ:1.00
 O B:SER8 2.3 9.8 1.0
O A:MET10 2.3 12.5 1.0
OXT B:MET10 2.3 11.4 1.0
O A:SER8 2.4 8.4 1.0
C A:SER8 3.4 6.8 1.0
C B:MET10 3.4 10.1 1.0
C A:MET10 3.4 7.7 1.0
C B:SER8 3.5 7.0 1.0
CA A:SER8 3.9 6.9 1.0
N B:MET10 3.9 7.6 1.0
C B:CYS9 3.9 8.0 1.0
N A:MET10 4.1 7.8 1.0
CB A:SER8 4.2 8.8 1.0
CA B:MET10 4.2 7.7 1.0
OXT A:MET10 4.2 6.7 0.6
O B:CYS9 4.3 9.6 1.0
O B:HOH2006 4.3 23.4 1.0
N B:CYS9 4.3 6.9 1.0
CA A:MET10 4.3 9.5 1.0
O B:MET10 4.3 19.4 1.0
CA B:CYS9 4.4 7.1 1.0
CA B:SER8 4.4 6.9 0.5
C A:CYS9 4.4 7.0 1.0
CA B:SER8 4.4 7.3 0.5
N A:CYS9 4.5 6.2 1.0
CB B:SER8 4.8 8.2 0.5
CA A:CYS9 4.8 6.5 1.0
O A:CYS9 4.9 9.7 1.0
CB A:MET10 4.9 14.1 0.6
CB B:SER8 4.9 7.3 0.5
CB A:MET10 5.0 18.2 0.4

Sodium binding site 3 out of 3 in 2xjh

Go back to Sodium Binding Sites List in 2xjh
Sodium binding site 3 out of 3 in the Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure and Copper-Binding Properties of Methanobactins From Methylosinus Trichosporium OB3B within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1002

b:10.3
occ:1.00
 O B:TYR5 2.5 8.5 1.0
O B:HOH2004 2.8 4.7 0.5
C B:TYR5 3.5 6.7 1.0
CD B:PRO6 4.0 7.0 1.0
CD2 B:TYR5 4.1 11.0 1.0
O B:HOH2002 4.1 6.4 0.6
N B:PRO6 4.2 5.8 1.0
CB B:TYR5 4.2 7.0 1.0
CA B:TYR5 4.4 6.4 1.0
CG B:TYR5 4.6 7.9 1.0
N B:TYR5 4.9 6.4 1.0

Reference:

A.El Ghazouani, A.Basle, S.J.Firbank, C.W.Knapp, J.Gray, D.W.Graham, C.Dennison. Copper-Binding Properties and Structures of Methanobactins From Methylosinus Trichosporium OB3B. Inorg.Chem. V. 50 1378 2011.
ISSN: ISSN 0020-1669
PubMed: 21254756
DOI: 10.1021/IC101965J
Page generated: Mon Oct 7 05:11:02 2024

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