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Cadmium in PDB 6scx: Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate

Enzymatic activity of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate

All present enzymatic activity of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate:
3.6.1.22;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate, PDB code: 6scx was solved by A.A.Mccarthy, K.M.Chen, H.Wu, L.Li, D.Homolka, P.Gos, F.Fleury-Olela, R.S.Pillai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 114.93 / 2.92
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 229.859, 229.859, 159.012, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 26

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate (pdb code 6scx). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 9 binding sites of Cadmium where determined in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate, PDB code: 6scx:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Cadmium binding site 1 out of 9 in 6scx

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Cadmium binding site 1 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd501

b:0.4
occ:1.00
 SG A:CYS307 2.3 1.0 1.0
SG A:CYS284 2.3 90.8 1.0
SG A:CYS287 2.3 90.3 1.0
SG A:CYS302 2.4 0.3 1.0
CB A:CYS307 3.3 0.1 1.0
CB A:CYS287 3.3 87.2 1.0
CB A:CYS284 3.3 87.1 1.0
CB A:CYS302 3.4 0.5 1.0
N A:CYS287 3.7 88.0 1.0
CA A:CYS287 4.0 88.2 1.0
OG A:SER309 4.2 0.1 1.0
CB A:THR286 4.5 88.5 1.0
CA A:CYS307 4.6 0.6 1.0
C A:THR286 4.7 91.1 1.0
N A:GLY288 4.7 93.8 1.0
CA A:CYS284 4.7 86.6 1.0
C A:CYS287 4.7 95.2 1.0
CB A:LYS304 4.8 0.4 1.0
CA A:CYS302 4.8 0.1 1.0
N A:ASN289 4.9 95.5 1.0
CA A:THR286 5.0 83.8 1.0
CB A:SER309 5.0 94.8 1.0

Cadmium binding site 2 out of 9 in 6scx

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Cadmium binding site 2 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd502

b:0.9
occ:0.83
 OE2 A:GLU374 2.6 96.5 1.0
O2A A:MGP505 2.8 50.5 0.7
O A:ALA354 3.3 70.8 1.0
CD A:GLU374 3.7 0.9 1.0
O2B A:MGP505 3.7 56.6 0.7
OE1 A:GLU415 3.8 0.9 1.0
OE1 A:GLU370 3.9 53.4 1.0
PA A:MGP505 4.1 53.8 0.7
NE2 A:GLN342 4.2 0.3 1.0
O1B A:MGP505 4.2 64.4 0.7
PB A:MGP505 4.3 62.1 0.7
OE1 A:GLU374 4.4 0.7 1.0
C A:ALA354 4.4 69.2 1.0
O3A A:MGP505 4.5 59.1 0.7
CG A:GLU374 4.5 92.4 1.0
O A:GLU415 4.5 0.8 1.0
CD A:CD503 4.7 0.0 0.9
CD A:GLU370 4.7 85.5 1.0
CD A:GLN342 4.8 0.3 1.0
CD A:GLU415 4.8 0.1 1.0
CA A:GLY355 4.8 62.8 1.0
CB A:GLU415 5.0 0.2 1.0

Cadmium binding site 3 out of 9 in 6scx

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Cadmium binding site 3 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd503

b:0.0
occ:0.90
 OE2 A:GLU370 3.1 82.6 1.0
OE1 A:GLU415 3.5 0.9 1.0
CD A:GLU370 4.0 85.5 1.0
OE1 A:GLU370 4.4 53.4 1.0
CD A:GLU415 4.5 0.1 1.0
O2A A:MGP505 4.6 50.5 0.7
CD A:CD502 4.7 0.9 0.8
N A:PHE356 4.7 59.2 1.0
NH1 A:ARG369 4.8 0.5 1.0
O1B A:MGP505 4.9 64.4 0.7
OE2 A:GLU415 4.9 0.8 1.0
O1A A:MGP505 4.9 55.1 0.7
CA A:GLY355 5.0 62.8 1.0

Cadmium binding site 4 out of 9 in 6scx

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Cadmium binding site 4 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd504

b:1.0
occ:1.00
 NE2 A:HIS251 1.9 0.7 1.0
NE2 C:HIS251 2.1 0.2 1.0
CE1 A:HIS251 2.6 0.9 1.0
CD2 C:HIS251 2.6 0.5 1.0
CE1 C:HIS251 3.1 0.7 1.0
CD2 A:HIS251 3.1 1.0 1.0
CG C:HIS251 3.8 0.9 1.0
ND1 A:HIS251 3.9 0.1 1.0
ND1 C:HIS251 4.0 0.3 1.0
CG A:HIS251 4.1 0.8 1.0

Cadmium binding site 5 out of 9 in 6scx

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Cadmium binding site 5 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd501

b:0.1
occ:1.00
 SG B:CYS307 2.1 0.2 1.0
SG B:CYS302 2.3 0.3 1.0
SG B:CYS284 2.4 91.5 1.0
SG B:CYS287 2.5 0.4 1.0
CB B:CYS307 3.1 0.0 1.0
CB B:CYS302 3.2 96.0 1.0
CB B:CYS284 3.3 87.5 1.0
CB B:CYS287 3.4 0.2 1.0
N B:CYS287 3.8 0.9 1.0
OG B:SER309 3.9 92.0 1.0
CA B:CYS287 4.2 0.4 1.0
CA B:CYS307 4.5 0.4 1.0
CB B:THR286 4.5 0.3 1.0
CA B:CYS302 4.7 95.0 1.0
CB B:LYS304 4.7 0.5 1.0
C B:THR286 4.7 0.9 1.0
CA B:CYS284 4.8 87.1 1.0
CB B:SER309 4.8 93.3 1.0
N B:GLY288 4.9 0.7 1.0
C B:CYS287 4.9 0.1 1.0
CA B:THR286 5.0 0.8 1.0

Cadmium binding site 6 out of 9 in 6scx

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Cadmium binding site 6 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd502

b:0.7
occ:0.75
 O2A B:MGP504 2.7 50.2 0.6
OE2 B:GLU374 2.8 1.0 1.0
O B:ALA354 3.3 63.3 1.0
O2B B:MGP504 3.6 52.0 0.6
OE1 B:GLU415 3.9 1.0 1.0
CD B:GLU374 3.9 1.0 1.0
NE2 B:GLN342 4.0 0.7 1.0
PA B:MGP504 4.0 51.6 0.6
O1B B:MGP504 4.0 52.8 0.6
OE1 B:GLU370 4.0 79.2 1.0
PB B:MGP504 4.1 53.1 0.6
O3A B:MGP504 4.3 52.4 0.6
C B:ALA354 4.5 63.7 1.0
CD B:GLN342 4.6 0.7 1.0
OE1 B:GLU374 4.6 0.2 1.0
O B:GLU415 4.6 0.6 1.0
CG B:GLU374 4.8 92.1 1.0
CA B:GLY355 4.9 60.0 1.0
CD B:GLU370 4.9 96.3 1.0
CD B:GLU415 4.9 0.9 1.0
O1A B:MGP504 5.0 53.8 0.6
O5' B:MGP504 5.0 51.9 0.6

Cadmium binding site 7 out of 9 in 6scx

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Cadmium binding site 7 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd503

b:0.9
occ:0.53
 NE2 B:HIS251 2.0 0.3 1.0
CD2 B:HIS251 2.5 0.5 1.0
CE1 B:HIS251 2.7 0.7 1.0
CG B:HIS251 3.3 0.1 1.0
ND1 B:HIS251 3.4 0.5 1.0
CB B:HIS251 4.6 0.0 1.0

Cadmium binding site 8 out of 9 in 6scx

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Cadmium binding site 8 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd501

b:0.8
occ:1.00
 SG C:CYS307 2.2 1.0 1.0
SG C:CYS287 2.4 0.4 1.0
SG C:CYS302 2.4 0.9 1.0
SG C:CYS284 2.5 93.9 1.0
CB C:CYS307 3.1 0.5 1.0
CB C:CYS287 3.3 0.9 1.0
CB C:CYS302 3.4 0.5 1.0
CB C:CYS284 3.5 90.1 1.0
N C:CYS287 3.8 0.6 1.0
CA C:CYS287 4.1 0.4 1.0
OG C:SER309 4.2 0.8 1.0
CA C:CYS307 4.4 0.8 1.0
CB C:THR286 4.5 0.9 1.0
CB C:LYS304 4.7 0.8 1.0
C C:THR286 4.7 0.1 1.0
C C:CYS287 4.8 0.3 1.0
CA C:CYS302 4.8 0.4 1.0
N C:GLY288 4.8 0.7 1.0
CA C:CYS284 4.9 89.9 1.0
CB C:SER309 4.9 0.1 1.0

Cadmium binding site 9 out of 9 in 6scx

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Cadmium binding site 9 out of 9 in the Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Crystal Structure of the Catalytic Domain of Human NUDT12 in Complex with 7-Methyl-Guanosine-5'-Triphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cd502

b:0.6
occ:0.98
 O2A C:MGP503 2.7 57.6 0.6
OE2 C:GLU374 2.8 0.7 1.0
O C:ALA354 3.2 76.8 1.0
O2B C:MGP503 3.4 61.2 0.6
CD C:GLU374 3.8 0.9 1.0
OE1 C:GLU415 3.9 0.6 1.0
O1B C:MGP503 3.9 65.0 0.6
PB C:MGP503 4.0 66.5 0.6
PA C:MGP503 4.0 60.5 0.6
OE1 C:GLU370 4.1 58.8 1.0
NE2 C:GLN342 4.1 0.3 1.0
O3A C:MGP503 4.3 63.9 0.6
C C:ALA354 4.4 77.0 1.0
OE1 C:GLU374 4.5 0.2 1.0
O C:GLU415 4.7 0.1 1.0
CD C:GLN342 4.7 0.9 1.0
CG C:GLU374 4.7 91.7 1.0
CA C:GLY355 4.8 74.4 1.0
CD C:GLU370 4.9 91.4 1.0
O1A C:MGP503 5.0 60.8 0.6

Reference:

H.Wu, L.Li, K.M.Chen, D.Homolka, P.Gos, F.Fleury-Olela, A.A.Mccarthy, R.S.Pillai. Decapping Enzyme NUDT12 Partners with Blmh For Cytoplasmic Surveillance of Nad-Capped Rnas. Cell Rep V. 29 4422 2019.
ISSN: ESSN 2211-1247
PubMed: 31875550
DOI: 10.1016/J.CELREP.2019.11.108
Page generated: Thu Jul 10 15:11:38 2025

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