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Zinc in PDB 3jbw: Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry)

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry) (pdb code 3jbw). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry), PDB code: 3jbw:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 3jbw

Go back to Zinc Binding Sites List in 3jbw
Zinc binding site 1 out of 2 in the Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:0.3
occ:1.00
CE1 A:HIS964 2.1 1.0 1.0
SG A:CYS749 2.2 0.8 1.0
CB A:CYS752 2.4 0.7 1.0
CB A:CYS749 2.4 0.8 1.0
NE2 A:HIS964 2.5 0.1 1.0
NE2 A:HIS959 2.6 0.3 1.0
CE1 A:HIS959 3.2 0.7 1.0
ND1 A:HIS964 3.3 0.2 1.0
N A:CYS752 3.3 0.5 1.0
CA A:CYS752 3.3 0.3 1.0
CD2 A:HIS959 3.8 0.9 1.0
SG A:CYS752 3.8 1.0 1.0
CD2 A:HIS964 3.8 0.9 1.0
CA A:CYS749 3.9 0.5 1.0
CG A:HIS964 4.1 0.9 1.0
C A:CYS752 4.1 0.6 1.0
C A:LEU751 4.2 0.1 1.0
OG A:SER754 4.4 0.2 1.0
O A:CYS752 4.5 0.8 1.0
ND1 A:HIS959 4.5 0.3 1.0
C A:CYS749 4.6 0.6 1.0
N A:LEU751 4.7 0.1 1.0
CD2 A:HIS766 4.7 0.9 1.0
N A:CYS749 4.8 0.4 1.0
CG A:HIS959 4.8 0.3 1.0
CB A:LEU751 4.8 0.7 1.0
CA A:LEU751 4.8 0.3 1.0
O A:LEU751 4.9 0.7 1.0
CG A:HIS766 5.0 0.4 1.0
N A:ASP753 5.0 0.0 1.0
CD1 A:ILE748 5.0 0.4 1.0

Zinc binding site 2 out of 2 in 3jbw

Go back to Zinc Binding Sites List in 3jbw
Zinc binding site 2 out of 2 in the Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Electron Microscopy Structure of Rag Paired Complex (with Nbd, No Symmetry) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:87.9
occ:1.00
NE2 C:HIS964 2.0 91.0 1.0
SG C:CYS749 2.3 0.6 1.0
CE1 C:HIS964 2.5 90.8 1.0
CB C:CYS749 2.5 0.2 1.0
NE2 C:HIS959 2.5 0.2 1.0
CB C:CYS752 2.6 88.7 1.0
CE1 C:HIS959 2.9 0.0 1.0
CD2 C:HIS964 3.2 84.1 1.0
CA C:CYS752 3.6 99.8 1.0
ND1 C:HIS964 3.7 92.1 1.0
N C:CYS752 3.7 0.0 1.0
CD2 C:HIS959 3.8 0.3 1.0
SG C:CYS752 3.9 76.5 1.0
CA C:CYS749 4.0 0.7 1.0
CG C:HIS964 4.1 93.9 1.0
ND1 C:HIS959 4.2 0.7 1.0
CD2 C:HIS766 4.2 0.6 1.0
C C:CYS752 4.3 98.0 1.0
CG C:HIS766 4.5 0.2 1.0
C C:LEU751 4.6 91.3 1.0
O C:CYS752 4.6 88.2 1.0
CG C:HIS959 4.7 0.3 1.0
CB C:HIS766 4.7 0.7 1.0
N C:CYS749 4.8 0.9 1.0
C C:CYS749 4.9 0.6 1.0
CB C:SER754 4.9 0.9 1.0
NE2 C:HIS766 4.9 0.1 1.0
CB C:ALA963 5.0 0.4 1.0

Reference:

H.Ru, M.G.Chambers, T.M.Fu, A.B.Tong, M.Liao, H.Wu. Molecular Mechanism of V(D)J Recombination From Synaptic RAG1-RAG2 Complex Structures. Cell(Cambridge,Mass.) V. 163 1138 2015.
ISSN: ISSN 0092-8674
PubMed: 26548953
DOI: 10.1016/J.CELL.2015.10.055
Page generated: Wed Dec 16 04:28:12 2020

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