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Zinc in PDB 2xr1: Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei

Protein crystallography data

The structure of Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei, PDB code: 2xr1 was solved by B.Mir-Montazeri, M.Ammelburg, D.Forouzan, A.N.Lupas, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.43 / 2.59
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.660, 97.720, 90.720, 90.00, 98.26, 90.00
R / Rfree (%) 20.919 / 26.678

Zinc Binding Sites:

The binding sites of Zinc atom in the Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei (pdb code 2xr1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei, PDB code: 2xr1:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2xr1

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Zinc binding site 1 out of 4 in the Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1638

b:49.8
occ:1.00
ND1 A:HIS244 2.0 45.5 1.0
NE2 A:HIS242 2.1 42.5 1.0
NE2 A:HIS329 2.3 47.7 1.0
OD2 A:ASP352 2.4 39.6 1.0
CE1 A:HIS244 2.9 48.1 1.0
CD2 A:HIS242 3.0 44.1 1.0
CE1 A:HIS242 3.0 41.8 1.0
CG A:HIS244 3.0 45.4 1.0
CD2 A:HIS329 3.1 47.5 1.0
ZN A:ZN1639 3.2 52.6 1.0
CG A:ASP352 3.4 42.4 1.0
CE1 A:HIS329 3.4 51.1 1.0
CB A:HIS244 3.5 43.4 1.0
CB A:ASP352 3.7 42.8 1.0
NE2 A:HIS247 4.0 37.8 1.0
NE2 A:HIS244 4.0 49.3 1.0
CD2 A:HIS247 4.1 36.8 1.0
CD2 A:HIS244 4.1 47.5 1.0
ND1 A:HIS242 4.1 39.7 1.0
CG A:HIS242 4.2 40.6 1.0
OD1 A:ASP246 4.2 50.1 1.0
CG A:HIS329 4.3 49.1 1.0
ND1 A:HIS329 4.4 51.0 1.0
OD1 A:ASP352 4.5 41.4 1.0
OD2 A:ASP246 4.6 44.7 1.0
CE1 A:HIS580 4.7 46.5 1.0
NE2 A:HIS580 4.7 47.6 1.0
CG A:ASP246 4.8 45.6 1.0
CA A:HIS244 4.9 43.2 1.0
CE1 A:HIS247 4.9 37.9 1.0

Zinc binding site 2 out of 4 in 2xr1

Go back to Zinc Binding Sites List in 2xr1
Zinc binding site 2 out of 4 in the Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1639

b:52.6
occ:1.00
OD2 A:ASP352 2.0 39.6 1.0
NE2 A:HIS247 2.1 37.8 1.0
NE2 A:HIS604 2.2 41.5 1.0
OD2 A:ASP246 2.3 44.7 1.0
CG A:ASP352 2.9 42.4 1.0
CD2 A:HIS247 3.0 36.8 1.0
CE1 A:HIS604 3.1 43.8 1.0
OD1 A:ASP352 3.2 41.4 1.0
ZN A:ZN1638 3.2 49.8 1.0
CE1 A:HIS247 3.2 37.9 1.0
CD2 A:HIS604 3.2 39.6 1.0
CG A:ASP246 3.2 45.6 1.0
OD1 A:ASP246 3.5 50.1 1.0
NE2 A:HIS242 4.1 42.5 1.0
CE1 A:HIS242 4.1 41.8 1.0
ND1 A:HIS604 4.2 43.3 1.0
CG A:HIS247 4.2 35.3 1.0
CG A:HIS604 4.3 40.5 1.0
ND1 A:HIS247 4.3 32.9 1.0
CB A:ASP352 4.3 42.8 1.0
CE1 A:HIS580 4.6 46.5 1.0
CB A:ASP246 4.6 43.2 1.0
ND1 A:HIS244 4.7 45.5 1.0
OH A:TYR536 4.9 62.8 1.0
NE2 A:HIS580 5.0 47.6 1.0
NE2 A:HIS329 5.0 47.7 1.0

Zinc binding site 3 out of 4 in 2xr1

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Zinc binding site 3 out of 4 in the Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1638

b:35.0
occ:1.00
ND1 B:HIS244 2.0 26.8 1.0
NE2 B:HIS242 2.2 26.6 1.0
NE2 B:HIS329 2.2 27.3 1.0
OD2 B:ASP352 2.3 20.5 1.0
CE1 B:HIS244 2.9 27.4 1.0
CD2 B:HIS242 3.1 28.2 1.0
CG B:HIS244 3.1 27.6 1.0
CD2 B:HIS329 3.1 26.7 1.0
CE1 B:HIS242 3.2 26.5 1.0
CE1 B:HIS329 3.2 28.6 1.0
ZN B:ZN1639 3.2 35.4 1.0
CG B:ASP352 3.4 24.5 1.0
CB B:HIS244 3.6 28.2 1.0
CB B:ASP352 3.7 23.5 1.0
O B:HOH2020 3.8 29.6 1.0
NE2 B:HIS247 4.0 23.9 1.0
NE2 B:HIS244 4.0 27.9 1.0
CD2 B:HIS247 4.1 24.0 1.0
CD2 B:HIS244 4.2 28.1 1.0
OD1 B:ASP246 4.2 35.9 1.0
CG B:HIS242 4.3 25.7 1.0
ND1 B:HIS242 4.3 25.3 1.0
CG B:HIS329 4.3 26.9 1.0
ND1 B:HIS329 4.3 27.3 1.0
OD1 B:ASP352 4.5 24.8 1.0
CE1 B:HIS580 4.6 25.0 1.0
OD2 B:ASP246 4.6 28.9 1.0
NE2 B:HIS580 4.7 25.3 1.0
CG B:ASP246 4.9 31.2 1.0
CE1 B:HIS247 5.0 24.5 1.0
CA B:HIS244 5.0 29.0 1.0

Zinc binding site 4 out of 4 in 2xr1

Go back to Zinc Binding Sites List in 2xr1
Zinc binding site 4 out of 4 in the Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor with N-Terminal Kh Domains (Kh-Cpsf) From Methanosarcina Mazei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1639

b:35.4
occ:1.00
OD2 B:ASP246 2.1 28.9 1.0
OD2 B:ASP352 2.1 20.5 1.0
NE2 B:HIS247 2.1 23.9 1.0
NE2 B:HIS604 2.2 25.1 1.0
CD2 B:HIS247 3.0 24.0 1.0
CE1 B:HIS604 3.1 26.1 1.0
CG B:ASP246 3.1 31.2 1.0
CG B:ASP352 3.1 24.5 1.0
CD2 B:HIS604 3.2 24.4 1.0
CE1 B:HIS247 3.2 24.5 1.0
ZN B:ZN1638 3.2 35.0 1.0
OD1 B:ASP246 3.3 35.9 1.0
OD1 B:ASP352 3.4 24.8 1.0
O B:HOH2020 3.6 29.6 1.0
O B:HOH2007 4.0 35.3 1.0
NE2 B:HIS242 4.1 26.6 1.0
ND1 B:HIS604 4.2 26.0 1.0
CG B:HIS247 4.2 23.8 1.0
CE1 B:HIS242 4.3 26.5 1.0
ND1 B:HIS247 4.3 20.9 1.0
CG B:HIS604 4.3 24.8 1.0
CB B:ASP352 4.5 23.5 1.0
CB B:ASP246 4.5 30.0 1.0
CE1 B:HIS580 4.8 25.0 1.0
ND1 B:HIS244 4.8 26.8 1.0
OH B:TYR536 4.9 41.6 1.0

Reference:

B.Mir-Montazeri, M.Ammelburg, D.Forouzan, A.N.Lupas, M.D.Hartmann. Crystal Structure of A Dimeric Archaeal Cleavage and Polyadenylation Specificity Factor. J.Struct.Biol. V. 173 191 2011.
ISSN: ISSN 1047-8477
PubMed: 20851187
DOI: 10.1016/J.JSB.2010.09.013
Page generated: Wed Dec 16 04:00:27 2020

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