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Zinc in PDB 5ejk: Crystal Structure of the Rous Sarcoma Virus Intasome

Enzymatic activity of Crystal Structure of the Rous Sarcoma Virus Intasome

All present enzymatic activity of Crystal Structure of the Rous Sarcoma Virus Intasome:
2.7.7.49; 2.7.7.7; 3.1.26.4;

Protein crystallography data

The structure of Crystal Structure of the Rous Sarcoma Virus Intasome, PDB code: 5ejk was solved by Z.Yin, K.Shi, S.Banerjee, H.Aihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.22 / 3.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 124.936, 157.854, 126.583, 90.00, 110.94, 90.00
R / Rfree (%) 25.4 / 29.5

Other elements in 5ejk:

The structure of Crystal Structure of the Rous Sarcoma Virus Intasome also contains other interesting chemical elements:

Tungsten (W) 36 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Rous Sarcoma Virus Intasome (pdb code 5ejk). 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 Rous Sarcoma Virus Intasome, PDB code: 5ejk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5ejk

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Zinc binding site 1 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:0.3
occ:1.00
ND1 A:HIS13 2.0 0.7 1.0
NE2 A:HIS9 2.0 0.8 1.0
SG A:CYS40 2.3 1.0 1.0
SG A:CYS37 2.4 0.8 1.0
CD2 A:HIS9 2.6 0.1 1.0
CE1 A:HIS13 2.9 0.4 1.0
CE1 A:HIS9 3.1 0.5 1.0
CG A:HIS13 3.1 0.4 1.0
CB A:CYS40 3.3 0.2 1.0
CB A:CYS37 3.3 0.8 1.0
CB A:HIS13 3.6 0.3 1.0
CG A:HIS9 3.8 0.4 1.0
ND1 A:HIS9 4.0 1.0 1.0
NE2 A:HIS13 4.0 0.2 1.0
CD2 A:HIS13 4.1 0.1 1.0
N A:CYS40 4.2 0.3 1.0
CA A:HIS13 4.2 0.8 1.0
CG1 E:VAL169 4.3 0.5 1.0
O A:HIS9 4.3 0.5 1.0
CA A:CYS40 4.3 0.7 1.0
CA A:CYS37 4.8 0.3 1.0
C A:HIS39 4.9 0.1 1.0

Zinc binding site 2 out of 8 in 5ejk

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Zinc binding site 2 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:0.7
occ:1.00
ND1 B:HIS13 2.0 0.5 1.0
NE2 B:HIS9 2.1 0.6 1.0
SG B:CYS40 2.3 0.6 1.0
SG B:CYS37 2.3 0.3 1.0
CD2 B:HIS9 2.7 0.4 1.0
CE1 B:HIS13 2.9 0.5 1.0
CE1 B:HIS9 3.1 1.0 1.0
CG B:HIS13 3.1 0.4 1.0
CB B:HIS13 3.5 0.3 1.0
CB B:CYS37 3.6 0.6 1.0
CB B:CYS40 3.7 0.0 1.0
CG B:HIS9 3.8 0.5 1.0
ND1 B:HIS9 3.9 0.1 1.0
NE2 B:HIS13 4.0 0.2 1.0
CA B:HIS13 4.1 0.4 1.0
CD2 B:HIS13 4.1 0.4 1.0
N B:CYS40 4.2 0.3 1.0
O B:HIS9 4.2 0.3 1.0
CA B:CYS40 4.5 0.1 1.0
C B:HIS39 4.6 0.7 1.0
CB B:HIS39 4.8 0.9 1.0
CG1 B:VAL169 4.8 0.2 1.0
CA B:CYS37 5.0 0.4 1.0
C B:HIS13 5.0 0.3 1.0
C B:HIS9 5.0 0.5 1.0

Zinc binding site 3 out of 8 in 5ejk

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Zinc binding site 3 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:0.4
occ:1.00
ND1 C:HIS13 2.1 0.9 1.0
NE2 C:HIS9 2.1 0.8 1.0
SG C:CYS37 2.4 1.0 1.0
SG C:CYS40 2.4 0.6 1.0
CE1 C:HIS9 2.7 0.8 1.0
CG C:HIS13 2.9 0.9 1.0
CB C:HIS13 3.0 0.7 1.0
CD2 C:HIS9 3.1 0.5 1.0
CE1 C:HIS13 3.2 0.6 1.0
CB C:CYS37 3.5 0.8 1.0
CB C:CYS40 3.5 0.5 1.0
CA C:HIS13 3.7 0.4 1.0
ND1 C:HIS9 3.8 0.5 1.0
CG C:HIS9 4.0 0.4 1.0
CD2 C:HIS13 4.1 0.8 1.0
NE2 C:HIS13 4.2 0.4 1.0
C C:HIS13 4.5 0.7 1.0
O C:HIS13 4.5 0.2 1.0
O C:HIS9 4.6 0.1 1.0
N C:CYS40 4.6 0.8 1.0
CG2 C:VAL169 4.6 0.7 1.0
CA C:CYS40 4.7 0.1 1.0
CA C:CYS37 4.9 0.2 1.0
N C:HIS13 4.9 0.3 1.0

Zinc binding site 4 out of 8 in 5ejk

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Zinc binding site 4 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:0.8
occ:1.00
NE2 D:HIS9 2.1 0.8 1.0
ND1 D:HIS13 2.1 0.9 1.0
SG D:CYS37 2.4 0.5 1.0
SG D:CYS40 2.5 0.8 1.0
CE1 D:HIS9 2.7 1.0 1.0
CB D:CYS37 3.0 0.4 1.0
CG D:HIS13 3.0 0.9 1.0
CE1 D:HIS13 3.1 0.7 1.0
CD2 D:HIS9 3.1 0.0 1.0
CB D:HIS13 3.3 0.7 1.0
ND1 D:HIS9 3.8 0.6 1.0
CB D:CYS40 4.0 0.0 1.0
CG D:HIS9 4.0 0.0 1.0
CA D:HIS13 4.0 0.0 1.0
CD2 D:HIS13 4.2 0.9 1.0
NE2 D:HIS13 4.2 0.1 1.0
CA D:CYS37 4.5 0.3 1.0
O D:HIS9 4.7 1.0 1.0
CG1 D:VAL169 4.7 0.1 1.0
C D:HIS13 4.8 0.2 1.0
O D:HIS13 4.9 0.4 1.0
N D:CYS40 5.0 0.1 1.0

Zinc binding site 5 out of 8 in 5ejk

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Zinc binding site 5 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn301

b:0.9
occ:1.00
ND1 E:HIS13 2.0 0.2 1.0
NE2 E:HIS9 2.0 0.4 1.0
SG E:CYS40 2.2 0.8 1.0
SG E:CYS37 2.3 0.1 1.0
CD2 E:HIS9 2.6 0.4 1.0
CE1 E:HIS13 2.9 0.3 1.0
CG E:HIS13 3.1 0.9 1.0
CE1 E:HIS9 3.1 0.1 1.0
CB E:CYS40 3.1 0.6 1.0
CB E:CYS37 3.5 0.6 1.0
CB E:HIS13 3.5 0.2 1.0
CG E:HIS9 3.7 0.3 1.0
ND1 E:HIS9 3.9 0.8 1.0
NE2 E:HIS13 4.0 0.6 1.0
CA E:HIS13 4.0 0.6 1.0
CD2 E:HIS13 4.1 0.5 1.0
O E:HIS9 4.1 0.8 1.0
N E:CYS40 4.1 0.2 1.0
CA E:CYS40 4.2 0.3 1.0
CG1 A:VAL169 4.5 0.9 1.0
C E:HIS9 4.9 0.1 1.0
CA E:CYS37 4.9 0.8 1.0
C E:HIS13 5.0 0.7 1.0

Zinc binding site 6 out of 8 in 5ejk

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Zinc binding site 6 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn301

b:0.2
occ:1.00
NE2 F:HIS9 2.0 0.2 1.0
ND1 F:HIS13 2.0 0.1 1.0
SG F:CYS40 2.3 0.9 1.0
SG F:CYS37 2.3 0.3 1.0
CD2 F:HIS9 2.7 0.8 1.0
CE1 F:HIS13 2.8 0.7 1.0
CB F:CYS37 3.0 0.4 1.0
CE1 F:HIS9 3.1 0.8 1.0
CG F:HIS13 3.2 0.9 1.0
CB F:HIS13 3.7 0.3 1.0
CG F:HIS9 3.8 0.3 1.0
ND1 F:HIS9 4.0 0.0 1.0
NE2 F:HIS13 4.0 0.8 1.0
CB F:CYS40 4.0 0.3 1.0
CD2 F:HIS13 4.2 0.4 1.0
CA F:HIS13 4.3 0.8 1.0
O F:HIS9 4.4 0.0 1.0
CG1 F:VAL169 4.5 0.4 1.0
CA F:CYS37 4.5 0.1 1.0
CA F:CYS40 4.6 0.5 1.0
N F:CYS40 4.6 0.7 1.0

Zinc binding site 7 out of 8 in 5ejk

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Zinc binding site 7 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn302

b:0.1
occ:1.00
NE2 G:HIS9 2.0 1.0 1.0
SG G:CYS37 2.3 0.9 1.0
SG G:CYS40 2.3 0.2 1.0
CE1 G:HIS9 2.4 0.3 1.0
ND1 G:HIS13 2.5 0.9 1.0
CB G:HIS13 2.7 0.7 1.0
CG G:HIS13 2.9 0.3 1.0
CD2 G:HIS9 3.1 0.3 1.0
CA G:HIS13 3.3 0.6 1.0
CB G:CYS37 3.4 0.2 1.0
ND1 G:HIS9 3.4 0.7 1.0
CE1 G:HIS13 3.7 0.3 1.0
CG G:HIS9 3.8 0.1 1.0
CB G:CYS40 3.8 0.3 1.0
O G:HIS13 3.9 1.0 1.0
C G:HIS13 3.9 0.8 1.0
CD2 G:HIS13 4.2 0.9 1.0
O G:HIS9 4.5 0.7 1.0
NE2 G:HIS13 4.6 0.3 1.0
N G:HIS13 4.6 0.5 1.0
N G:CYS40 4.8 0.7 1.0
CA G:CYS37 4.8 0.1 1.0
CA G:CYS40 4.9 0.7 1.0
N G:ILE14 5.0 0.4 1.0

Zinc binding site 8 out of 8 in 5ejk

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Zinc binding site 8 out of 8 in the Crystal Structure of the Rous Sarcoma Virus Intasome


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 Rous Sarcoma Virus Intasome within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn301

b:0.9
occ:1.00
ND1 H:HIS13 2.0 0.8 1.0
NE2 H:HIS9 2.0 0.7 1.0
SG H:CYS37 2.3 0.8 1.0
SG H:CYS40 2.3 1.0 1.0
CD2 H:HIS9 2.8 0.0 1.0
CG H:HIS13 2.9 0.4 1.0
CE1 H:HIS9 2.9 0.2 1.0
CE1 H:HIS13 3.1 0.1 1.0
CB H:HIS13 3.2 0.0 1.0
CB H:CYS37 3.5 0.5 1.0
CA H:HIS13 3.8 0.4 1.0
CG H:HIS9 3.8 0.7 1.0
ND1 H:HIS9 3.9 0.1 1.0
CB H:CYS40 3.9 0.3 1.0
CD2 H:HIS13 4.1 0.8 1.0
NE2 H:HIS13 4.1 0.8 1.0
O H:HIS9 4.3 0.5 1.0
N H:CYS40 4.4 0.8 1.0
C H:HIS13 4.6 0.5 1.0
CA H:CYS40 4.7 0.1 1.0
O H:HIS13 4.7 0.4 1.0
CA H:CYS37 4.9 0.9 1.0
N H:HIS13 4.9 0.6 1.0

Reference:

Z.Yin, K.Shi, S.Banerjee, K.K.Pandey, S.Bera, D.P.Grandgenett, H.Aihara. Crystal Structure of the Rous Sarcoma Virus Intasome. Nature V. 530 362 2016.
ISSN: ESSN 1476-4687
PubMed: 26887497
DOI: 10.1038/NATURE16950
Page generated: Wed Dec 16 06:10:06 2020

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