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

Protein crystallography data

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

Other elements in 6kq1:

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

Iron (Fe) 2 atoms

Zinc Binding Sites:

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 6kq1

Go back to Zinc Binding Sites List in 6kq1
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 6kq1

Go back to Zinc Binding Sites List in 6kq1
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 6kq1

Go back to Zinc Binding Sites List in 6kq1
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 6kq1

Go back to Zinc Binding Sites List in 6kq1
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 6kq1

Go back to Zinc Binding Sites List in 6kq1
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

Reference:

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.
Page generated: Wed Dec 16 12:08:57 2020

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