Cadmium in PDB 1zps: Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi

All present enzymatic activity of Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi:
3.5.4.19;

The structure of Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi, PDB code: 1zps was solved by J.Sivaraman, R.S.Myers, L.Boju, T.Sulea, M.Cygler, V.J.Davisson, J.D.Schrag, Montreal-Kingston Bacterial Structural Genomicsinitiative (Bsgi), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.90 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.783, 54.358, 117.362, 90.00, 90.00, 90.00
R / Rfree (%)	20.7 / 23.5

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Cadmium atom in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi (pdb code 1zps). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 binding sites of Cadmium where determined in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi, PDB code: 1zps:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2606 b:18.6 occ:1.00 OD2 A:ASP85 2.1 20.2 1.0 OD1 A:ASP89 2.2 21.1 1.0 OD1 A:ASP87 2.2 21.2 1.0 O B:HOH619 2.4 29.5 1.0 O A:HOH607 2.6 14.7 1.0 OD2 A:ASP87 2.8 22.4 1.0 CG A:ASP87 2.9 21.6 1.0 CG A:ASP85 3.1 23.0 1.0 CG A:ASP89 3.1 21.3 1.0 OD2 A:ASP89 3.3 19.0 1.0 OD1 A:ASP85 3.8 22.6 1.0 CD A:CD2611 3.8 53.3 1.0 CD A:CD2607 3.9 27.8 1.0 CB A:ASP85 4.0 22.1 1.0 O B:HOH511 4.1 18.5 1.0 CB A:ASP87 4.3 21.9 1.0 O A:HOH618 4.4 38.8 1.0 CB A:ASP89 4.5 18.5 1.0 CB A:ALA90 4.5 19.4 1.0 N A:ASP89 4.6 19.2 1.0 O B:VAL39 4.7 15.6 1.0 C A:ASP89 4.8 18.3 1.0 N A:ALA90 4.8 18.5 1.0 CA A:ASP89 4.8 18.7 1.0 N A:ASP87 4.8 19.2 1.0 O A:HOH615 5.0 23.1 1.0

Cadmium binding site 2 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2607 b:27.8 occ:1.00 O B:HOH511 2.3 18.5 1.0 O A:HOH615 2.3 23.1 1.0 O A:HOH607 2.4 14.7 1.0 OD1 A:ASP85 2.5 22.6 1.0 SG B:CYS109 2.7 21.1 1.0 OD2 A:ASP85 3.1 20.2 1.0 CG A:ASP85 3.2 23.0 1.0 CB B:CYS109 3.3 18.1 1.0 CD B:CD2617 3.6 19.9 1.0 SG A:CYS86 3.8 19.7 1.0 CD A:CD2606 3.9 18.6 1.0 O B:HOH629 4.3 15.3 1.0 O B:VAL39 4.4 15.6 1.0 CB B:MET38 4.4 14.5 1.0 OD1 A:ASP87 4.5 21.2 1.0 O B:HOH619 4.6 29.5 1.0 CB A:ASP85 4.7 22.1 1.0 N B:VAL39 4.7 14.0 1.0 CA B:CYS109 4.7 17.8 1.0 N A:CYS86 4.8 20.4 1.0 CA B:MET38 4.9 13.3 1.0

Cadmium binding site 3 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2610 b:34.5 occ:1.00 O A:HOH633 1.9 27.2 1.0 O A:HOH632 2.2 39.0 1.0 NE2 A:HIS57 2.3 21.5 1.0 CE1 A:HIS57 3.3 23.3 1.0 CD2 A:HIS57 3.3 25.5 1.0 NH1 A:ARG49 4.1 43.2 1.0 CD2 A:LEU68 4.2 30.6 1.0 ND1 A:HIS57 4.4 23.9 1.0 CD A:ARG49 4.4 35.1 1.0 CG A:HIS57 4.4 24.2 1.0 CB A:LEU68 4.6 30.3 1.0 O A:HOH548 4.8 29.0 1.0 CG A:LEU68 4.9 29.0 1.0

Cadmium binding site 4 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2611 b:53.3 occ:1.00 OD2 A:ASP89 2.2 19.0 1.0 O A:HOH618 2.8 38.8 1.0 O B:HOH616 2.9 41.2 1.0 O A:HOH617 3.2 40.0 1.0 CG A:ASP89 3.3 21.3 1.0 OD1 A:ASP89 3.7 21.1 1.0 O B:HOH619 3.7 29.5 1.0 NE2 A:HIS16 3.8 47.6 1.0 CD A:CD2606 3.8 18.6 1.0 OD2 A:ASP87 3.9 22.4 1.0 CE1 A:HIS16 3.9 47.9 1.0 CB A:ASP89 4.5 18.5 1.0 NE A:ARG15 4.7 45.5 1.0 CD2 A:HIS16 4.8 48.0 1.0 ND1 A:HIS16 4.9 48.1 1.0 OG1 B:THR61 5.0 34.0 1.0 CG A:ASP87 5.0 21.6 1.0 NH2 A:ARG15 5.0 47.0 1.0

Cadmium binding site 5 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2613 b:51.3 occ:1.00 O A:HOH625 1.9 17.3 1.0 OE2 A:GLU35 2.3 27.7 1.0 OE1 A:GLU35 2.5 27.8 1.0 O A:HOH610 2.5 32.4 1.0 O A:HOH611 2.7 16.2 1.0 CD A:GLU35 2.7 27.1 1.0 CB A:ARG107 3.8 23.9 1.0 CG A:ARG107 3.9 29.4 1.0 O A:ASP124 4.0 30.9 1.0 CG A:GLU35 4.2 22.9 1.0 CB A:SER108 4.3 17.0 1.0 O A:HOH606 4.4 36.3 1.0 O A:HOH602 4.4 36.6 1.0 N A:SER108 4.5 16.9 1.0 O A:HOH529 4.5 26.1 1.0 N A:VAL126 4.5 31.8 1.0 CA A:ALA125 4.7 30.6 1.0 CA A:ARG107 4.9 20.8 1.0 C A:ASP124 5.0 31.2 1.0 C A:ARG107 5.0 18.9 1.0

Cadmium binding site 6 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2614 b:50.1 occ:1.00 NE2 A:HIS75 2.4 31.3 1.0 O A:HOH628 2.6 35.9 1.0 O A:HOH627 2.7 43.4 1.0 CD2 A:HIS75 3.3 31.4 1.0 CE1 A:HIS75 3.5 32.4 1.0 CG A:HIS75 4.4 30.9 1.0 ND1 A:HIS75 4.5 32.2 1.0 O A:SER73 4.7 35.3 1.0 CA A:GLY99 4.8 27.7 1.0

Cadmium binding site 7 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2616 b:16.3 occ:1.00 SG A:CYS102 2.4 18.8 1.0 SG B:CYS86 2.5 13.9 1.0 OXT A:ACY803 2.6 22.4 1.0 SG A:CYS109 2.6 15.8 1.0 O A:ACY803 2.6 25.8 1.0 C A:ACY803 2.9 21.6 1.0 CB A:CYS102 3.3 17.8 1.0 CB B:CYS86 3.4 15.2 1.0 CB A:CYS109 3.5 13.6 1.0 CD B:CD2603 3.6 16.8 1.0 CA A:CYS102 3.6 20.2 1.0 CD2 A:HIS103 3.9 19.0 1.0 CA A:CYS109 3.9 14.8 1.0 NE2 A:HIS103 4.0 18.7 1.0 N A:HIS103 4.2 19.5 1.0 O A:HOH514 4.3 17.8 1.0 O A:HOH549 4.4 17.9 1.0 CH3 A:ACY803 4.4 23.6 1.0 C A:CYS102 4.4 19.1 1.0 OXT A:ACY804 4.6 25.1 1.0 OD1 B:ASP85 4.6 15.3 1.0 CA B:CYS86 4.7 13.9 1.0 O A:HOH545 4.7 6.4 1.0 N A:CYS102 4.8 18.7 1.0 O A:ALA101 4.8 19.4 1.0 CG A:HIS103 4.8 18.6 1.0 CE1 A:HIS103 4.8 20.2 1.0 N B:CYS86 4.9 12.6 1.0 N A:CYS109 4.9 15.2 1.0

Cadmium binding site 8 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2618 b:44.6 occ:1.00 O A:HOH631 2.1 28.8 1.0 OE1 A:GLU52 2.4 38.3 1.0 O A:HOH634 2.5 30.3 1.0 OE2 A:GLU52 2.9 37.8 1.0 CD A:GLU52 3.0 37.4 1.0 CD A:ARG48 3.8 36.8 1.0 CG A:ARG48 3.9 35.4 1.0 OE2 A:GLU45 3.9 40.8 1.0 CG A:GLU52 4.5 35.6 1.0 CB A:ARG48 4.8 31.0 1.0 CD A:GLU45 4.9 38.7 1.0

Cadmium binding site 9 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


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 Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd2619 b:56.1 occ:1.00 O A:HOH591 2.2 37.3 1.0 OD1 A:ASP22 2.6 36.3 1.0 OD2 A:ASP22 2.8 38.9 1.0 CG A:ASP22 3.0 36.8 1.0 OD1 A:ASN17 4.1 52.7 1.0 CB A:ASP22 4.5 34.8 1.0 N A:ASP22 4.9 37.2 1.0 CG A:ASN17 5.0 51.6 1.0

Cadmium binding site 10 out of 19 in the Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi within 5.0Å range: probe atom residue distance (Å) B Occ B:Cd2601 b:16.8 occ:1.00 OE2 B:GLU52 2.2 16.3 1.0 O B:HOH501 2.6 7.3 1.0 OE1 B:GLU52 2.7 15.8 1.0 CD B:GLU52 2.8 16.8 1.0 O B:HOH541 4.1 20.1 1.0 CG B:GLU52 4.3 15.7 1.0 NH1 B:ARG48 4.4 18.2 1.0 NH2 B:ARG48 4.5 19.5 1.0 CZ B:ARG48 5.0 17.2 1.0 O B:HOH551 5.0 31.4 1.0

J.Sivaraman, R.S.Myers, L.Boju, T.Sulea, M.Cygler, V.J.Davisson, J.D.Schrag. Crystal Structure of Methanobacterium Thermoautotrophicum Phosphoribosyl-Amp Cyclohydrolase Hisi. Biochemistry V. 44 10071 2005.
ISSN: ISSN 0006-2960
PubMed: 16042384
DOI: 10.1021/BI050472W