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Zinc in PDB 3ebe: Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain

Protein crystallography data

The structure of Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain, PDB code: 3ebe was solved by E.M.Warren, B.F.Eichman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.40 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.565, 94.414, 69.775, 90.00, 112.79, 90.00
R / Rfree (%) 20.2 / 24.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain (pdb code 3ebe). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain, PDB code: 3ebe:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3ebe

Go back to Zinc Binding Sites List in 3ebe
Zinc binding site 1 out of 3 in the Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal 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 Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:41.4
occ:1.00
ND1 A:HIS406 2.0 50.8 1.0
SG A:CYS403 2.2 47.1 1.0
SG A:CYS381 2.3 41.7 1.0
SG A:CYS391 2.3 46.6 1.0
CE1 A:HIS406 2.8 52.4 1.0
CB A:CYS381 3.1 43.5 1.0
CG A:HIS406 3.1 53.3 1.0
CB A:CYS391 3.2 46.5 1.0
CB A:CYS403 3.4 47.5 1.0
CB A:HIS406 3.6 53.6 1.0
NE2 A:HIS406 4.0 51.6 1.0
N A:CYS403 4.0 48.0 1.0
CD2 A:HIS406 4.2 51.4 1.0
CB A:GLN393 4.3 51.4 1.0
CA A:CYS403 4.3 48.0 1.0
CB A:ALA383 4.4 41.6 1.0
CG A:GLN393 4.5 54.9 1.0
N A:HIS406 4.5 54.1 1.0
CA A:CYS381 4.5 43.5 1.0
CA A:CYS391 4.7 47.4 1.0
CA A:HIS406 4.7 54.4 1.0
C A:CYS403 5.0 48.8 1.0

Zinc binding site 2 out of 3 in 3ebe

Go back to Zinc Binding Sites List in 3ebe
Zinc binding site 2 out of 3 in the Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal 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 Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:49.4
occ:1.00
ND1 B:HIS406 2.0 48.5 1.0
SG B:CYS391 2.3 51.4 1.0
SG B:CYS403 2.4 48.5 1.0
SG B:CYS381 2.4 47.3 1.0
CE1 B:HIS406 2.9 50.3 1.0
CG B:HIS406 3.1 50.8 1.0
CB B:CYS381 3.1 47.6 1.0
CB B:CYS391 3.3 54.7 1.0
CB B:CYS403 3.5 47.1 1.0
CB B:HIS406 3.5 52.7 1.0
N B:CYS403 4.0 47.0 1.0
NE2 B:HIS406 4.1 49.6 1.0
CD2 B:HIS406 4.2 49.8 1.0
CB B:ALA383 4.2 51.4 1.0
CB B:GLN393 4.2 54.2 1.0
CG B:GLN393 4.3 55.2 1.0
CA B:CYS403 4.3 48.0 1.0
N B:HIS406 4.4 52.6 1.0
CA B:CYS381 4.6 48.8 1.0
CA B:HIS406 4.6 53.4 1.0
CA B:CYS391 4.8 55.3 1.0
C B:CYS403 4.9 48.6 1.0
CB B:TYR405 4.9 52.1 1.0

Zinc binding site 3 out of 3 in 3ebe

Go back to Zinc Binding Sites List in 3ebe
Zinc binding site 3 out of 3 in the Crystal Structure of Xenopus Laevis Replication Initiation Factor MCM10 Internal 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 Xenopus Laevis Replication Initiation Factor MCM10 Internal Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:50.9
occ:1.00
ND1 C:HIS406 2.0 49.2 1.0
SG C:CYS403 2.3 49.6 1.0
SG C:CYS381 2.3 52.0 1.0
SG C:CYS391 2.4 55.9 1.0
CE1 C:HIS406 2.9 51.9 1.0
CB C:CYS381 3.0 52.6 1.0
CG C:HIS406 3.1 50.4 1.0
CB C:CYS391 3.3 57.7 1.0
CB C:CYS403 3.4 51.1 1.0
CB C:HIS406 3.5 51.0 1.0
N C:CYS403 4.0 51.4 1.0
NE2 C:HIS406 4.1 52.2 1.0
CD2 C:HIS406 4.2 50.2 1.0
CB C:GLN393 4.2 56.8 1.0
CA C:CYS403 4.3 51.2 1.0
CG C:GLN393 4.4 59.1 1.0
CA C:CYS381 4.5 52.6 1.0
N C:HIS406 4.5 52.7 1.0
CB C:ALA383 4.6 57.5 1.0
CA C:HIS406 4.6 51.5 1.0
CA C:CYS391 4.7 58.0 1.0
C C:CYS403 5.0 51.4 1.0

Reference:

E.M.Warren, S.Vaithiyalingam, J.Haworth, B.Greer, A.K.Bielinsky, W.J.Chazin, B.F.Eichman. Structural Basis For Dna Binding By Replication Initiator MCM10. Structure V. 16 1892 2008.
ISSN: ISSN 0969-2126
PubMed: 19081065
DOI: 10.1016/J.STR.2008.10.005
Page generated: Wed Dec 16 04:15:27 2020

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