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Zinc in PDB 2rjb: Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276

Protein crystallography data

The structure of Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276, PDB code: 2rjb was solved by J.Seetharaman, Y.Chen, D.Wang, Y.Fang, K.Cunningham, L.-C.Ma, R.Xia, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt, Northeaststructural Genomics Consortium (Nesg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.12 / 2.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 192.209, 76.387, 159.052, 90.00, 116.55, 90.00
R / Rfree (%) 23.3 / 28.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276 (pdb code 2rjb). 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 Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276, PDB code: 2rjb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 2rjb

Go back to Zinc Binding Sites List in 2rjb
Zinc binding site 1 out of 4 in the Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276


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 Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.2
occ:1.00
CE1 A:HIS224 2.2 22.5 1.0
OE1 A:GLU290 2.3 36.3 1.0
NE2 A:HIS224 2.4 23.6 1.0
NE2 A:HIS68 2.6 27.3 1.0
CD A:GLU290 3.1 34.3 1.0
CE1 A:HIS68 3.2 25.4 1.0
OE2 A:GLU290 3.3 36.4 1.0
ND1 A:HIS224 3.5 26.4 1.0
CD2 A:HIS68 3.6 25.4 1.0
CD2 A:HIS224 3.8 23.5 1.0
ND1 A:HIS68 4.2 26.0 1.0
CG A:HIS224 4.3 23.9 1.0
OG1 A:THR226 4.3 19.6 1.0
CE2 A:PHE388 4.3 15.0 1.0
OE1 A:GLN264 4.4 28.4 1.0
CG A:HIS68 4.5 25.9 1.0
O A:HOH646 4.5 55.4 1.0
CG A:GLU290 4.6 28.7 1.0
CB A:ALA70 4.6 13.2 1.0
CD2 A:PHE388 4.8 12.6 1.0

Zinc binding site 2 out of 4 in 2rjb

Go back to Zinc Binding Sites List in 2rjb
Zinc binding site 2 out of 4 in the Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276


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 Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:22.2
occ:1.00
OE1 B:GLU290 2.1 28.8 1.0
NE2 B:HIS224 2.3 25.6 1.0
OE2 B:GLU290 2.5 36.1 1.0
CD B:GLU290 2.6 35.3 1.0
NE2 B:HIS68 2.6 37.9 1.0
CD2 B:HIS224 3.1 27.4 1.0
CE1 B:HIS224 3.3 26.7 1.0
CE1 B:HIS68 3.4 39.3 1.0
CD2 B:HIS68 3.6 37.0 1.0
O B:HOH629 3.9 66.0 1.0
CG B:GLU290 4.1 32.0 1.0
CG B:HIS224 4.3 26.4 1.0
OG1 B:THR226 4.3 26.3 1.0
ND1 B:HIS224 4.3 29.2 1.0
OE1 B:GLN264 4.4 27.7 1.0
CE2 B:PHE388 4.6 17.0 1.0
ND1 B:HIS68 4.6 37.4 1.0
CB B:ALA70 4.7 18.6 1.0
CB B:GLU290 4.7 31.5 1.0
CG B:HIS68 4.7 36.7 1.0
CD2 B:PHE388 5.0 18.1 1.0

Zinc binding site 3 out of 4 in 2rjb

Go back to Zinc Binding Sites List in 2rjb
Zinc binding site 3 out of 4 in the Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276


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 Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn503

b:22.2
occ:1.00
OE1 C:GLU290 2.2 41.5 1.0
NE2 C:HIS68 2.2 44.8 1.0
NE2 C:HIS224 2.4 57.1 1.0
CE1 C:HIS68 2.7 45.0 1.0
CD C:GLU290 2.8 43.9 1.0
OE2 C:GLU290 2.9 42.8 1.0
CE1 C:HIS224 3.3 57.1 1.0
CD2 C:HIS68 3.4 43.2 1.0
CD2 C:HIS224 3.4 57.0 1.0
ND1 C:HIS68 4.0 43.7 1.0
OG1 C:THR226 4.0 47.8 1.0
O C:HOH567 4.2 51.8 1.0
CG C:GLU290 4.3 44.9 1.0
CG C:HIS68 4.3 44.0 1.0
NE2 C:GLN264 4.4 44.5 1.0
ND1 C:HIS224 4.4 56.8 1.0
CG C:HIS224 4.5 55.8 1.0
CB C:ALA70 4.6 41.3 1.0
CB C:GLU290 4.7 45.3 1.0
CE2 C:PHE388 4.8 35.6 1.0
CD2 C:PHE388 5.0 37.2 1.0

Zinc binding site 4 out of 4 in 2rjb

Go back to Zinc Binding Sites List in 2rjb
Zinc binding site 4 out of 4 in the Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276


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 Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. Northeast Structural Genomics Consortium Target SFR276 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn504

b:22.2
occ:1.00
OE1 D:GLU290 2.4 60.9 1.0
OE2 D:GLU290 2.5 62.0 1.0
NE2 D:HIS224 2.6 60.0 1.0
CD D:GLU290 2.8 60.4 1.0
CE1 D:HIS224 3.0 60.8 1.0
NE2 D:HIS68 3.2 62.5 1.0
CE1 D:HIS68 3.8 62.7 1.0
CD2 D:HIS224 3.9 60.0 1.0
CE2 D:PHE388 4.2 53.7 1.0
CG D:GLU290 4.3 58.9 1.0
ND1 D:HIS224 4.3 60.9 1.0
CD2 D:HIS68 4.4 62.6 1.0
OE1 D:GLN264 4.5 33.3 1.0
CD2 D:PHE388 4.6 53.4 1.0
OG1 D:THR226 4.7 60.9 1.0
CG D:HIS224 4.7 60.7 1.0
CB D:ALA70 4.8 63.1 1.0
CB D:GLU290 4.9 56.4 1.0

Reference:

J.Seetharaman, Y.Chen, D.Wang, Y.Fang, K.Cunningham, L.-C.Ma, R.Xia, J.Liu, M.C.Baran, T.B.Acton, B.Rost, G.T.Montelione, L.Tong, J.F.Hunt. Crystal Structure of Uncharacterized Protein Ydcj (SF1787) From Shigella Flexneri Which Includes Domain DUF1338. To Be Published.
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