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Cadmium in PDB 5wyf: Structure of Amino Acid Racemase, 2.12 A

Enzymatic activity of Structure of Amino Acid Racemase, 2.12 A

All present enzymatic activity of Structure of Amino Acid Racemase, 2.12 A:
5.1.1.21;

Protein crystallography data

The structure of Structure of Amino Acid Racemase, 2.12 A, PDB code: 5wyf was solved by H.Sakuraba, Y.Mutaguchi, J.Hayashi, T.Ohshima, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.12
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.514, 85.277, 186.566, 90.00, 96.93, 90.00
R / Rfree (%) 17.6 / 22.1

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Cadmium atom in the Structure of Amino Acid Racemase, 2.12 A (pdb code 5wyf). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 36 binding sites of Cadmium where determined in the Structure of Amino Acid Racemase, 2.12 A, PDB code: 5wyf:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 36 in 5wyf

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Cadmium binding site 1 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1002

b:40.7
occ:1.00
OD2 A:ASP5 2.4 41.4 1.0
CG A:ASP5 3.1 33.6 1.0
OD1 A:ASP5 3.1 29.3 1.0
CB A:ASP5 4.5 34.4 1.0
CA A:GLY2 4.5 47.6 1.0

Cadmium binding site 2 out of 36 in 5wyf

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Cadmium binding site 2 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1003

b:61.4
occ:1.00
NE2 A:HIS33 2.5 41.1 1.0
O A:HOH1222 2.6 43.6 1.0
CD2 A:HIS33 3.4 38.2 1.0
CE1 A:HIS33 3.5 43.2 1.0
O A:HOH1219 3.6 25.4 1.0
CG2 A:VAL40 4.2 37.4 1.0
CG A:HIS33 4.5 41.3 1.0
ND1 A:HIS33 4.6 43.2 1.0
NZ A:LYS46 4.6 65.1 1.0
CE A:LYS46 4.8 56.2 1.0
CB A:VAL40 5.0 35.8 1.0

Cadmium binding site 3 out of 36 in 5wyf

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Cadmium binding site 3 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1004

b:46.8
occ:1.00
NE2 A:HIS35 2.4 36.8 1.0
O A:HOH1221 2.4 40.7 1.0
CD2 A:HIS35 3.3 36.1 1.0
CE1 A:HIS35 3.4 34.9 1.0
O A:HOH1223 3.4 32.1 1.0
O A:HOH1197 3.5 35.7 1.0
ND1 A:HIS35 4.5 34.1 1.0
CG A:HIS35 4.5 35.2 1.0

Cadmium binding site 4 out of 36 in 5wyf

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Cadmium binding site 4 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1005

b:41.8
occ:1.00
OE1 A:GLU64 2.5 41.4 1.0
OE2 A:GLU64 2.5 37.2 1.0
O A:HOH1223 2.7 32.1 1.0
CD A:GLU64 2.8 35.6 1.0
O A:HOH1221 4.2 40.7 1.0
CG A:GLU64 4.3 37.7 1.0

Cadmium binding site 5 out of 36 in 5wyf

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Cadmium binding site 5 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1006

b:48.6
occ:1.00
ND1 A:HIS188 2.2 43.9 1.0
OE2 A:GLU231 2.5 34.1 1.0
OE1 A:GLU231 2.6 34.7 1.0
CD A:GLU231 2.8 35.7 1.0
CE1 A:HIS188 3.2 47.8 1.0
CG A:HIS188 3.2 42.4 1.0
CB A:HIS188 3.5 42.0 1.0
NE2 A:HIS188 4.3 43.4 1.0
CG A:GLU231 4.3 36.7 1.0
CD2 A:HIS188 4.4 41.5 1.0
CA A:HIS188 4.5 41.9 1.0

Cadmium binding site 6 out of 36 in 5wyf

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Cadmium binding site 6 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1007

b:62.5
occ:1.00
O A:HOH1216 2.3 50.9 1.0
NE2 A:HIS243 2.4 28.4 1.0
CE1 A:HIS243 3.2 29.6 1.0
CD2 A:HIS243 3.5 34.0 1.0
ND1 A:HIS243 4.4 36.4 1.0
CG A:HIS243 4.6 34.0 1.0
O A:HOH1224 4.9 23.6 1.0

Cadmium binding site 7 out of 36 in 5wyf

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Cadmium binding site 7 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1008

b:53.0
occ:1.00
OE2 A:GLU435 2.3 40.0 1.0
ND1 A:HIS354 2.3 47.2 1.0
O A:ARG353 2.4 41.8 1.0
OE1 A:GLU435 2.6 45.1 1.0
O A:HOH1218 2.7 42.9 1.0
CD A:GLU435 2.8 44.0 1.0
CE1 A:HIS354 3.1 45.2 1.0
CG A:HIS354 3.3 42.2 1.0
C A:ARG353 3.4 45.0 1.0
CA A:HIS354 3.6 44.4 1.0
CB A:HIS354 3.8 42.5 1.0
N A:HIS354 4.0 46.1 1.0
NE2 A:HIS354 4.1 49.9 1.0
CD2 A:HIS354 4.3 44.9 1.0
CG A:GLU435 4.3 40.7 1.0
CD A:PRO355 4.5 45.8 1.0
CA A:ARG353 4.6 45.0 1.0
CB A:ARG353 4.6 47.7 1.0
OG1 A:THR432 4.6 53.5 1.0
C A:HIS354 4.9 44.2 1.0

Cadmium binding site 8 out of 36 in 5wyf

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Cadmium binding site 8 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1009

b:69.3
occ:1.00
OD2 A:ASP381 2.5 43.3 1.0
OD1 A:ASP381 2.9 38.1 1.0
CG A:ASP381 3.0 38.3 1.0
OD2 A:ASP383 3.9 49.6 1.0
CB A:ALA384 4.4 34.3 1.0
CB A:ASP381 4.5 38.6 1.0
CG A:LYS373 4.6 46.4 1.0
N A:ALA384 4.6 38.3 1.0
CB A:ASP383 4.7 43.9 1.0
CG A:ASP383 4.7 47.5 1.0
CE A:LYS373 4.7 49.9 1.0
CD A:LYS373 4.9 48.6 1.0

Cadmium binding site 9 out of 36 in 5wyf

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Cadmium binding site 9 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1010

b:51.2
occ:1.00
NE2 A:HIS395 2.5 53.4 1.0
CD2 A:HIS395 3.4 43.5 1.0
CE1 A:HIS395 3.5 48.9 1.0
CG A:HIS395 4.6 52.4 1.0
ND1 A:HIS395 4.6 47.4 1.0
OH A:TYR391 4.7 41.1 1.0
CE2 A:TYR391 4.8 38.6 1.0

Cadmium binding site 10 out of 36 in 5wyf

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Cadmium binding site 10 out of 36 in the Structure of Amino Acid Racemase, 2.12 A


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Structure of Amino Acid Racemase, 2.12 A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1011

b:71.9
occ:1.00
OE2 A:GLU95 2.4 55.7 1.0
OE1 A:GLU95 2.8 43.5 1.0
CD A:GLU95 2.9 42.5 1.0
OE1 B:GLU13 3.0 49.9 1.0
CD B:GLU13 4.0 53.1 1.0
NZ A:LYS99 4.2 47.9 1.0
CG A:GLU95 4.3 40.0 1.0
CG B:GLU13 4.5 55.4 1.0
CE2 B:TYR17 4.6 42.3 1.0
OH B:TYR17 4.8 41.8 1.0
CB B:GLU13 5.0 42.8 1.0
OE2 B:GLU13 5.0 58.6 1.0

Reference:

J.Hayashi, Y.Mutaguchi, Y.Minemura, N.Nakagawa, K.Yoneda, T.Ohmori, T.Ohshima, H.Sakuraba. Crystal Structure of the Novel Amino-Acid Racemase Isoleucine 2-Epimerase From Lactobacillus Buchneri. Acta Crystallogr D Struct V. 73 428 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28471367
DOI: 10.1107/S2059798317005332
Page generated: Sat Dec 12 08:27:58 2020

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