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Zinc in PDB 1v15: Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)

Enzymatic activity of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)

All present enzymatic activity of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A):
3.1.21.1;

Protein crystallography data

The structure of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A), PDB code: 1v15 was solved by M.J.Mate, C.Kleanthous, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.54 / 2.4
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 93.145, 123.310, 110.531, 90.00, 90.00, 90.00
R / Rfree (%) 24.2 / 32.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) (pdb code 1v15). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A), PDB code: 1v15:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 1v15

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Zinc binding site 1 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


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 the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1132

b:88.0
occ:1.00
 OP1 E:DC6 1.9 66.2 1.0
NE2 A:HIS131 2.1 69.3 1.0
NE2 A:HIS127 2.2 75.7 1.0
ND1 A:HIS102 2.4 76.4 1.0
O3' E:DT5 2.8 69.3 1.0
CE1 A:HIS131 2.9 70.1 1.0
P E:DC6 2.9 66.7 1.0
CE1 A:HIS102 3.1 76.1 1.0
CD2 A:HIS127 3.1 76.3 1.0
CE1 A:HIS127 3.2 76.5 1.0
CG A:HIS102 3.2 76.7 1.0
CD2 A:HIS131 3.3 69.8 1.0
CB A:HIS102 3.7 77.4 1.0
CA A:HIS102 3.8 77.4 1.0
N A:ALA103 4.0 76.8 1.0
OP2 E:DC6 4.0 68.2 1.0
NE2 A:HIS102 4.0 76.2 1.0
O5' E:DC6 4.0 67.7 1.0
ND1 A:HIS131 4.1 70.5 1.0
CD2 A:HIS102 4.1 76.5 1.0
C3' E:DT5 4.1 71.5 1.0
C5' E:DC6 4.3 66.8 1.0
ND1 A:HIS127 4.3 77.3 1.0
CG A:HIS127 4.3 76.9 1.0
CG A:HIS131 4.3 70.9 1.0
C A:HIS102 4.4 77.2 1.0
C4' E:DT5 4.6 71.8 1.0
O A:ALA103 4.7 76.4 1.0

Zinc binding site 2 out of 8 in 1v15

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Zinc binding site 2 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


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 the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1135

b:66.5
occ:1.00
 NE2 B:HIS127 2.0 65.3 1.0
NE2 B:HIS131 2.1 62.4 1.0
OP1 G:DC6 2.1 66.8 1.0
ND1 B:HIS102 2.3 65.9 1.0
CE1 B:HIS131 2.9 63.5 1.0
CD2 B:HIS127 3.0 64.6 1.0
CE1 B:HIS127 3.1 64.7 1.0
CE1 B:HIS102 3.1 66.5 1.0
O G:HOH2006 3.2 71.3 1.0
CD2 B:HIS131 3.2 63.4 1.0
P G:DC6 3.3 64.3 1.0
O3' G:DT5 3.3 65.7 1.0
CG B:HIS102 3.3 65.7 1.0
CB B:HIS102 3.7 65.3 1.0
CA B:HIS102 3.8 65.4 1.0
N B:ALA103 3.9 65.2 1.0
ND1 B:HIS131 4.1 63.5 1.0
ND1 B:HIS127 4.1 66.5 1.0
CG B:HIS127 4.1 63.9 1.0
CG B:HIS131 4.3 64.5 1.0
NE2 B:HIS102 4.3 65.1 1.0
OP2 G:DC6 4.3 65.2 1.0
O5' G:DC6 4.4 64.0 1.0
C B:HIS102 4.4 65.5 1.0
O B:ALA103 4.4 65.7 1.0
CD2 B:HIS102 4.4 65.7 1.0
C5' G:DC6 4.5 61.9 1.0
C3' G:DT5 4.5 68.2 1.0
C4' G:DT5 4.8 69.4 1.0
CA B:ALA103 5.0 65.2 1.0

Zinc binding site 3 out of 8 in 1v15

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Zinc binding site 3 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


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 the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1132

b:67.8
occ:1.00
 OP1 I:DC6 1.8 69.5 1.0
ND1 C:HIS102 2.0 58.8 1.0
NE2 C:HIS127 2.1 63.6 1.0
NE2 C:HIS131 2.1 54.8 1.0
CE1 C:HIS102 2.7 53.8 1.0
CD2 C:HIS127 3.0 64.1 1.0
CE1 C:HIS131 3.1 56.6 1.0
P I:DC6 3.1 69.8 1.0
CD2 C:HIS131 3.1 56.6 1.0
CG C:HIS102 3.1 59.8 1.0
CE1 C:HIS127 3.2 61.4 1.0
O3' I:DT5 3.4 68.7 1.0
CB C:HIS102 3.7 60.6 1.0
O5' I:DC6 3.7 69.8 1.0
NE2 C:HIS102 3.9 54.1 1.0
CA C:HIS102 4.0 61.7 1.0
N C:ALA103 4.0 61.8 1.0
CD2 C:HIS102 4.1 55.9 1.0
CG C:HIS127 4.2 64.5 1.0
ND1 C:HIS131 4.2 57.1 1.0
ND1 C:HIS127 4.2 61.5 1.0
CG C:HIS131 4.3 57.2 1.0
O C:ALA103 4.3 62.6 1.0
OP2 I:DC6 4.3 70.8 1.0
C3' I:DT5 4.4 69.2 1.0
C C:HIS102 4.4 61.9 1.0
C4' I:DT5 4.7 69.3 1.0
CA C:ALA103 4.9 61.9 1.0
C C:ALA103 4.9 62.2 1.0

Zinc binding site 4 out of 8 in 1v15

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Zinc binding site 4 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


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 the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1135

b:65.5
occ:1.00
 OP1 K:DC6 1.9 72.0 1.0
NE2 D:HIS131 2.0 70.8 1.0
NE2 D:HIS127 2.2 63.4 1.0
ND1 D:HIS102 2.3 69.5 1.0
CE1 D:HIS131 2.8 71.8 1.0
CE1 D:HIS102 3.0 69.4 1.0
P K:DC6 3.0 70.5 1.0
CE1 D:HIS127 3.1 62.8 1.0
CD2 D:HIS131 3.1 71.5 1.0
O3' K:DT5 3.2 69.0 1.0
CD2 D:HIS127 3.2 64.6 1.0
CG D:HIS102 3.4 69.1 1.0
N D:ALA103 3.8 68.1 1.0
O K:HOH2003 3.8 75.0 1.0
CA D:HIS102 3.8 68.2 1.0
CB D:HIS102 3.9 68.5 1.0
OP2 K:DC6 3.9 70.2 1.0
ND1 D:HIS131 4.0 71.9 1.0
CG D:HIS131 4.2 72.0 1.0
C3' K:DT5 4.2 69.4 1.0
NE2 D:HIS102 4.2 70.0 1.0
ND1 D:HIS127 4.2 64.7 1.0
O5' K:DC6 4.3 69.7 1.0
CG D:HIS127 4.3 67.1 1.0
C D:HIS102 4.3 68.1 1.0
CD2 D:HIS102 4.4 69.2 1.0
C4' K:DT5 4.4 69.9 1.0
C5' K:DC6 4.5 69.0 1.0
CA D:ALA103 4.8 68.4 1.0
O D:ALA103 4.9 68.6 1.0
C5' K:DT5 5.0 71.1 1.0

Zinc binding site 5 out of 8 in 1v15

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Zinc binding site 5 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


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 the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn1009

b:80.4
occ:1.00
 O E:HOH2004 1.9 48.3 1.0
N7 E:DG3 2.0 74.3 1.0
OP2 L:DC10 2.4 66.9 1.0
C8 E:DG3 2.9 74.1 1.0
O3' L:DG9 3.1 68.6 1.0
C5 E:DG3 3.1 74.6 1.0
P L:DC10 3.3 66.6 1.0
O6 E:DG3 3.5 74.7 1.0
C6 E:DG3 3.6 74.4 1.0
N9 E:DG3 4.2 74.5 1.0
O5' L:DC10 4.2 66.8 1.0
C4 E:DG3 4.2 74.8 1.0
C3' L:DG9 4.4 69.4 1.0
OP1 L:DC10 4.5 67.1 1.0
C5' L:DG9 4.9 70.2 1.0
C4' L:DG9 5.0 69.7 1.0

Zinc binding site 6 out of 8 in 1v15

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Zinc binding site 6 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn1009

b:61.7
occ:1.00
 O G:HOH2009 1.7 38.6 1.0
OP2 J:DC10 2.2 61.0 1.0
N7 G:DG3 2.3 66.2 1.0
C8 G:DG3 3.2 66.6 1.0
C5 G:DG3 3.3 67.3 1.0
O6 G:DG3 3.6 66.8 1.0
P J:DC10 3.6 60.1 1.0
C6 G:DG3 3.8 67.2 1.0
OP1 J:DC10 4.1 62.5 1.0
N9 G:DG3 4.4 67.7 1.0
C4 G:DG3 4.5 67.8 1.0
O5' J:DC10 4.5 62.1 1.0
O5' J:DG9 4.5 60.3 1.0
O3' J:DG9 4.6 59.5 1.0
C5' J:DG9 4.8 59.2 1.0
N6 G:DA4 4.8 66.0 1.0

Zinc binding site 7 out of 8 in 1v15

Go back to Zinc Binding Sites List in 1v15
Zinc binding site 7 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1009

b:73.9
occ:1.00
 OP2 H:DC10 2.1 63.9 1.0
N7 I:DG3 2.2 69.8 1.0
O I:HOH2006 3.1 67.5 1.0
C8 I:DG3 3.2 69.2 1.0
C5 I:DG3 3.3 69.2 1.0
P H:DC10 3.6 64.2 1.0
O6 I:DG3 3.6 68.7 1.0
C6 I:DG3 3.8 68.6 1.0
O5' H:DC10 4.3 62.0 1.0
OP1 H:DC10 4.4 60.6 1.0
N9 I:DG3 4.4 69.6 1.0
C4 I:DG3 4.4 68.9 1.0
O3' H:DG9 4.6 64.6 1.0
OP2 I:DG3 4.6 85.3 1.0
N6 I:DA4 4.7 66.7 1.0
O5' H:DG9 4.9 70.6 1.0
C5' H:DG9 5.0 68.1 1.0
C3' H:DG9 5.0 66.6 1.0

Zinc binding site 8 out of 8 in 1v15

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Zinc binding site 8 out of 8 in the Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Colicin E9, Mutant HIS103ALA, in Complex with Zn+2 and Dsdna (Resolution 2.4A) within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1009

b:91.5
occ:1.00
 N7 K:DG3 1.9 67.2 1.0
OP2 F:DC10 2.5 70.0 1.0
C8 K:DG3 2.9 67.6 1.0
C5 K:DG3 3.0 67.4 1.0
O6 K:DG3 3.3 67.0 1.0
C6 K:DG3 3.5 67.8 1.0
P F:DC10 3.5 70.3 1.0
OP1 F:DC10 3.8 69.5 1.0
N9 K:DG3 4.1 67.8 1.0
C4 K:DG3 4.1 67.1 1.0
O5' F:DC10 4.5 70.8 1.0
OP1 K:DG3 4.6 76.8 1.0
O3' F:DG9 4.7 69.5 1.0
N1 K:DG3 4.9 68.1 1.0
O5' F:DG9 5.0 69.6 1.0

Reference:

M.J.Mate, C.Kleanthous. Structure-Based Analysis of the Metal-Dependent Mechanism of H-N-H Endonucleases J.Biol.Chem. V. 279 34763 2004.
ISSN: ISSN 0021-9258
PubMed: 15190054
DOI: 10.1074/JBC.M403719200
Page generated: Mon Jan 25 16:14:53 2021

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