Zinc in PDB 6kq1: Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1.

The structure of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1., PDB code: 6kq1 was solved by S.Fujii, H.Oki, K.Kawahara, T.Ohkubo, M.Masanari-Fujii, S.Wakai, Y.Sambongi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 1.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	50.787, 52.017, 62.393, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22.4

The structure of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. (pdb code 6kq1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1., PDB code: 6kq1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:16.3 occ:1.00 OD2 A:ASP2 2.0 16.6 1.0 OE1 A:GLU4 2.0 21.8 1.0 CG A:ASP2 2.8 18.2 1.0 CD A:GLU4 2.9 40.0 1.0 OD1 A:ASP2 2.9 17.8 1.0 CG A:GLU4 3.1 27.7 1.0 OE2 A:GLU4 4.1 33.8 1.0 O A:HOH260 4.1 21.2 1.0 CB A:ASP2 4.2 17.4 1.0 CB A:GLU4 4.7 20.1 1.0 O A:HOH269 4.7 33.3 1.0 N A:ALA5 5.0 16.2 1.0

Zinc binding site 2 out of 5 in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:23.0 occ:0.50 OE2 A:GLU70 2.0 25.5 1.0 NZ A:LYS10 2.1 25.3 1.0 O A:HOH252 2.2 41.4 1.0 O A:HOH268 2.3 38.5 1.0 OE1 A:GLU70 2.3 23.9 1.0 CD A:GLU70 2.5 26.1 1.0 CE A:LYS10 2.9 18.3 1.0 O A:HOH271 4.1 38.8 1.0 CG A:GLU70 4.1 24.6 1.0 O A:HOH209 4.2 30.4 1.0 CD A:LYS10 4.3 19.2 1.0 O A:PRO65 4.4 20.1 1.0 NE2 A:GLN1 4.9 31.2 1.0 CG2 A:THR67 5.0 25.3 1.0 CD2 A:LEU6 5.0 16.9 1.0

Zinc binding site 3 out of 5 in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:16.5 occ:1.00 OD1 B:ASP2 2.0 17.8 1.0 OE1 B:GLU4 2.0 21.8 1.0 CG B:ASP2 2.8 18.2 1.0 OD2 B:ASP2 2.9 16.6 1.0 CD B:GLU4 2.9 40.0 1.0 CG B:GLU4 3.2 27.7 1.0 OE2 B:GLU4 4.1 33.8 1.0 O B:HOH251 4.1 20.2 1.0 CB B:ASP2 4.2 17.4 1.0 CB B:GLU4 4.7 20.1 1.0 N B:ALA5 4.9 16.2 1.0 O B:HOH278 4.9 33.2 1.0

Zinc binding site 4 out of 5 in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:26.9 occ:0.50 OD1 B:ASP19 1.7 48.0 1.0 O B:HOH243 2.4 33.0 1.0 CG B:ASP19 2.5 46.1 1.0 OD2 B:ASP19 2.8 48.9 1.0 CB B:ASP19 3.9 34.3 1.0 O B:ASP19 4.1 46.9 1.0 CD B:LYS28 4.2 42.7 1.0 CB B:LYS28 4.4 23.9 1.0 CA B:ASP19 4.4 30.4 1.0 OE1 B:GLU29 4.5 55.5 1.0 C B:ASP19 4.8 38.4 1.0 CG B:LYS28 4.9 27.9 1.0

Zinc binding site 5 out of 5 in the Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Cytochrome C551 From Pseudomonas Sp. Strain Mt-1. within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn103 b:25.4 occ:0.50 NZ B:LYS10 2.1 25.3 1.0 OE2 B:GLU70 2.1 25.5 1.0 O B:HOH272 2.2 37.8 1.0 O B:HOH228 2.2 42.8 1.0 OE1 B:GLU70 2.3 23.9 1.0 CD B:GLU70 2.5 26.1 1.0 CE B:LYS10 2.9 18.3 1.0 O B:HOH281 4.0 44.0 1.0 CG B:GLU70 4.1 24.6 1.0 O B:HOH252 4.1 37.1 1.0 O B:HOH206 4.2 38.2 1.0 O B:PRO65 4.2 20.1 1.0 CD B:LYS10 4.4 19.2 1.0 CG2 B:THR67 4.8 25.3 1.0 CA B:VAL66 4.9 18.3 1.0 N B:THR67 4.9 16.9 1.0 O B:HOH293 4.9 42.9 1.0 CD2 B:LEU6 5.0 16.9 1.0 NE2 B:GLN1 5.0 31.2 1.0

S.Fujii, H.Oki, K.Kawahara, T.Ohkubo, M.Masanari-Fujii, S.Wakai, Y.Sambongi. Structural Insights Into High Stability of Cytochrome C551 From A Deep-Sea Piezo-Tolerant Bacterium, Pseudomonas Sp. Strain Mt-1 To Be Published.