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Cadmium in PDB 1ng1: N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus

Protein crystallography data

The structure of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus, PDB code: 1ng1 was solved by D.M.Freymann, R.M.Stroud, P.Walter, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.03
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.072, 100.072, 73.490, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 25

Cadmium Binding Sites:

The binding sites of Cadmium atom in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus (pdb code 1ng1). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 3 binding sites of Cadmium where determined in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus, PDB code: 1ng1:
Jump to Cadmium binding site number: 1; 2; 3;

Cadmium binding site 1 out of 3 in 1ng1

Go back to Cadmium Binding Sites List in 1ng1
Cadmium binding site 1 out of 3 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd701

b:15.4
occ:1.00
OE2 A:GLU11 2.4 13.8 1.0
OE2 A:GLU33 2.4 18.2 1.0
OE1 A:GLU11 2.4 15.8 1.0
OE1 A:GLU33 2.5 17.2 1.0
CD A:GLU33 2.7 16.8 1.0
CD A:GLU11 2.7 17.4 1.0
CD A:ARG15 4.1 9.3 1.0
CG A:GLU33 4.2 16.1 1.0
CG A:GLU11 4.2 17.2 1.0
O A:HOH976 4.3 12.8 1.0
NH1 A:ARG15 4.4 8.8 1.0
O A:HOH1125 4.4 30.3 1.0
O A:HOH1063 4.7 31.0 1.0
NE A:ARG15 4.9 11.7 1.0
O A:HOH1105 4.9 25.5 1.0
CZ A:ARG15 5.0 12.3 1.0
CG A:ARG15 5.0 11.2 1.0

Cadmium binding site 2 out of 3 in 1ng1

Go back to Cadmium Binding Sites List in 1ng1
Cadmium binding site 2 out of 3 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd751

b:29.6
occ:0.50
OE2 A:GLU285 2.4 36.4 1.0
OE1 A:GLU285 2.5 38.7 1.0
CD A:GLU285 2.7 32.4 1.0
O A:HOH1074 3.9 26.9 1.0
O A:HOH1107 4.0 38.2 1.0
CG A:GLU285 4.2 25.4 1.0
O A:HOH1144 4.3 43.2 1.0
NZ A:LYS83 4.5 16.1 1.0
O A:HOH1137 4.9 20.6 1.0

Cadmium binding site 3 out of 3 in 1ng1

Go back to Cadmium Binding Sites List in 1ng1
Cadmium binding site 3 out of 3 in the N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of N and Gtpase Domains of the Signal Sequence Recognition Protein Ffh From Thermus Aquaticus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd752

b:38.8
occ:0.50
NE2 A:HIS261 2.3 23.6 1.0
O A:ACY952 2.5 38.5 1.0
OXT A:ACY952 2.6 41.3 1.0
C A:ACY952 2.8 43.2 1.0
O A:HOH1126 2.9 60.9 1.0
O A:HOH1127 3.0 46.1 1.0
CE1 A:HIS261 3.3 21.0 1.0
CD2 A:HIS261 3.3 18.7 1.0
CH3 A:ACY952 4.4 40.5 1.0
ND1 A:HIS261 4.4 19.6 1.0
ND2 A:ASN44 4.4 17.1 1.0
CG A:HIS261 4.5 17.1 1.0
CB A:GLU46 4.9 15.3 1.0
OD1 A:ASN44 4.9 17.1 1.0

Reference:

D.M.Freymann, R.J.Keenan, R.M.Stroud, P.Walter. Functional Changes in the Structure of the Srp Gtpase on Binding Gdp and MG2+Gdp. Nat.Struct.Biol. V. 6 793 1999.
ISSN: ISSN 1072-8368
PubMed: 10426959
DOI: 10.1038/11572
Page generated: Fri Aug 28 12:16:09 2020
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