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Zinc in PDB 3woo: Crystal Structure of the Dap Bii Hexapeptide Complex I

Protein crystallography data

The structure of Crystal Structure of the Dap Bii Hexapeptide Complex I, PDB code: 3woo was solved by Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, T.Nonaka, W.Ogasawara, N.Tanaka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.92 / 1.80
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 121.700, 121.700, 218.970, 90.00, 90.00, 90.00
R / Rfree (%) 18.2 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Dap Bii Hexapeptide Complex I (pdb code 3woo). 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 the Dap Bii Hexapeptide Complex I, PDB code: 3woo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3woo

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Zinc binding site 1 out of 4 in the Crystal Structure of the Dap Bii Hexapeptide Complex I


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 the Dap Bii Hexapeptide Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn809

b:32.6
occ:1.00
O A:HOH1436 2.1 28.8 1.0
NE2 A:HIS665 2.1 28.3 1.0
NZ A:LYS47 2.9 52.2 1.0
CE1 A:HIS665 3.0 28.5 1.0
CD2 A:HIS665 3.2 27.1 1.0
ND1 A:HIS665 4.1 24.7 1.0
CG A:HIS665 4.3 25.8 1.0
CE A:LYS47 4.4 43.7 1.0
CG A:LYS47 4.4 33.6 1.0
NE2 A:GLN259 4.5 41.3 1.0
OE1 A:GLN259 4.7 38.5 1.0
CD A:LYS47 4.9 35.7 1.0
CB A:LYS47 5.0 24.3 1.0

Zinc binding site 2 out of 4 in 3woo

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Zinc binding site 2 out of 4 in the Crystal Structure of the Dap Bii Hexapeptide Complex I


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 the Dap Bii Hexapeptide Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn810

b:48.6
occ:1.00
NZ A:LYS508 2.1 23.3 1.0
O A:HOH1433 2.4 44.1 1.0
OE1 A:GLU505 2.5 27.4 1.0
CE A:LYS508 3.0 24.4 1.0
CD A:GLU505 3.2 26.4 1.0
OE2 A:GLU505 3.2 28.4 1.0
CD A:LYS508 3.8 24.5 1.0
CG A:GLU505 4.7 26.7 1.0
O A:HOH1455 4.9 28.9 1.0

Zinc binding site 3 out of 4 in 3woo

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Zinc binding site 3 out of 4 in the Crystal Structure of the Dap Bii Hexapeptide Complex I


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 the Dap Bii Hexapeptide Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn805

b:51.1
occ:1.00
NE2 B:HIS665 2.2 40.9 1.0
CE1 B:HIS665 2.4 40.2 1.0
NZ B:LYS47 2.5 53.5 1.0
CD2 B:HIS665 3.5 38.3 1.0
ND1 B:HIS665 3.7 41.7 1.0
CE B:LYS47 3.8 51.1 1.0
CD B:LYS47 3.9 48.4 1.0
CG B:HIS665 4.3 35.0 1.0
NE2 B:GLN259 4.7 39.8 1.0
CG B:LYS47 4.7 41.9 1.0
CB B:LYS47 4.8 37.9 1.0
OE1 B:GLN259 4.9 40.0 1.0

Zinc binding site 4 out of 4 in 3woo

Go back to Zinc Binding Sites List in 3woo
Zinc binding site 4 out of 4 in the Crystal Structure of the Dap Bii Hexapeptide Complex I


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 the Dap Bii Hexapeptide Complex I within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn806

b:49.6
occ:1.00
OE2 B:GLU505 2.2 38.5 1.0
O B:HOH1294 2.3 36.5 1.0
NZ B:LYS508 2.4 31.1 1.0
CE B:LYS508 2.7 32.4 1.0
CD B:GLU505 2.8 34.6 1.0
OE1 B:GLU505 2.9 34.3 1.0
CD B:LYS508 4.2 31.9 1.0
CG B:GLU505 4.3 31.7 1.0
O B:HOH1187 4.8 35.6 1.0

Reference:

Y.Sakamoto, Y.Suzuki, I.Iizuka, C.Tateoka, S.Roppongi, M.Fujimoto, K.Inaka, H.Tanaka, M.Masaki, K.Ohta, H.Okada, T.Nonaka, Y.Morikawa, K.T.Nakamura, W.Ogasawara, N.Tanaka. S46 Peptidases Are the First Exopeptidases to Be Members of Clan Pa Sci Rep V. 4 4977 2014.
ISSN: ESSN 2045-2322
PubMed: 24827749
DOI: 10.1038/SREP04977
Page generated: Wed Dec 16 04:57:52 2020

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