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Zinc in PDB 3qqc: Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain

Protein crystallography data

The structure of Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain, PDB code: 3qqc was solved by F.W.Martinez-Rucobo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.70 / 3.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 168.570, 107.040, 51.090, 90.00, 97.10, 90.00
R / Rfree (%) 19.3 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain (pdb code 3qqc). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain, PDB code: 3qqc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3qqc

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Zinc binding site 1 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2000

b:0.9
occ:1.00
SG A:CYS208 2.4 0.6 1.0
SG A:CYS164 2.5 0.5 1.0
SG A:CYS161 2.5 0.6 1.0
CB A:CYS161 3.0 0.8 1.0
CD A:PRO209 3.5 0.8 1.0
CB A:CYS208 3.6 0.9 1.0
CA A:CYS208 3.8 0.3 1.0
N A:PRO209 3.9 0.5 1.0
C A:CYS208 4.1 1.0 1.0
O A:PRO209 4.1 0.9 1.0
CB A:CYS164 4.2 0.0 1.0
CA A:CYS161 4.5 0.6 1.0
CB A:ARG166 4.6 0.6 1.0
O A:ARG162 4.6 0.9 1.0
C A:PRO209 4.6 0.1 1.0
N A:ARG166 4.8 0.8 1.0
CG A:PRO209 4.8 0.5 1.0
CA A:PRO209 4.8 0.8 1.0
O A:CYS208 5.0 0.5 1.0
N A:GLY165 5.0 0.6 1.0

Zinc binding site 2 out of 4 in 3qqc

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Zinc binding site 2 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2001

b:0.7
occ:1.00
NE2 A:HIS134 2.2 0.5 1.0
SG A:CYS131 2.5 0.1 1.0
SG A:CYS121 2.5 0.7 1.0
SG A:CYS124 2.6 0.7 1.0
CD2 A:HIS134 3.0 0.4 1.0
CE1 A:HIS134 3.3 0.9 1.0
CB A:CYS121 3.7 0.4 1.0
O A:PRO132 3.8 0.0 1.0
CB A:CYS131 3.9 0.4 1.0
CG A:HIS134 4.2 0.3 1.0
CB A:CYS124 4.3 0.7 1.0
ND1 A:HIS134 4.4 0.6 1.0
CA A:GLY113 4.4 0.7 1.0
CA A:CYS131 4.7 0.8 1.0
N A:GLU122 4.8 0.4 1.0
N A:VAL114 4.8 0.7 1.0
CG2 A:VAL114 4.8 0.3 1.0
C A:CYS131 4.9 0.5 1.0
C A:PRO132 4.9 1.0 1.0
N A:GLY113 5.0 0.0 1.0

Zinc binding site 3 out of 4 in 3qqc

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Zinc binding site 3 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2002

b:0.6
occ:1.00
SG A:CYS11 2.3 89.6 1.0
SG A:CYS26 2.3 0.1 1.0
SG A:CYS8 2.3 0.2 1.0
SG A:CYS29 2.3 0.8 1.0
CB A:CYS26 2.9 99.9 1.0
CB A:CYS8 3.2 99.1 1.0
CB A:CYS29 3.5 96.6 1.0
CB A:CYS11 3.6 85.4 1.0
N A:CYS29 3.9 95.6 1.0
N A:CYS11 3.9 86.3 1.0
CA A:CYS29 4.1 97.0 1.0
CB A:GLU31 4.2 0.2 1.0
CA A:CYS11 4.3 84.4 1.0
CA A:CYS26 4.4 0.9 1.0
CB A:ASN10 4.4 92.5 1.0
CB A:HIS13 4.6 87.2 1.0
C A:CYS29 4.6 0.6 1.0
CA A:CYS8 4.7 98.9 1.0
N A:GLU31 4.7 0.9 1.0
OD1 A:ASN10 4.7 0.7 1.0
C A:CYS11 4.8 85.0 1.0
C A:ASN10 4.9 91.1 1.0
N A:GLY30 4.9 0.3 1.0
N A:HIS13 5.0 84.3 1.0
CB A:VAL28 5.0 95.1 1.0
CA A:ASN10 5.0 90.7 1.0

Zinc binding site 4 out of 4 in 3qqc

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Zinc binding site 4 out of 4 in the Crystal Structure of Archaeal SPT4/5 Bound to the Rnap Clamp Domain


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 Archaeal SPT4/5 Bound to the Rnap Clamp Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn100

b:0.8
occ:1.00
SG E:CYS18 2.4 1.0 1.0
SG E:CYS9 2.4 0.1 1.0
SG E:CYS6 2.4 0.5 1.0
SG E:CYS21 2.5 0.7 1.0
CB E:CYS18 2.8 0.5 1.0
CB E:CYS6 3.1 0.8 1.0
CB E:CYS21 4.1 0.9 1.0
CB E:CYS9 4.1 0.2 1.0
CB E:SER23 4.3 0.8 1.0
CA E:CYS18 4.3 0.8 1.0
N E:CYS9 4.4 0.9 1.0
N E:SER23 4.5 0.0 1.0
CA E:CYS6 4.6 0.6 1.0
N E:CYS21 4.6 0.0 1.0
N E:GLY22 4.7 0.8 1.0
O E:CYS18 4.8 1.0 1.0
CA E:CYS9 4.8 0.1 1.0
CA E:CYS21 4.8 0.3 1.0
C E:CYS18 4.8 0.9 1.0
CB E:TYR11 4.9 0.5 1.0
CA E:SER23 4.9 0.2 1.0

Reference:

F.W.Martinez-Rucobo, S.Sainsbury, A.C.Cheung, P.Cramer. Architecture of the Rna Polymerase-SPT4/5 Complex and Basis of Universal Transcription Processivity. Embo J. V. 30 1302 2011.
ISSN: ISSN 0261-4189
PubMed: 21386817
DOI: 10.1038/EMBOJ.2011.64
Page generated: Wed Dec 16 04:45:53 2020

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