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Gadolinium in PDB 4phb: Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative

Protein crystallography data

The structure of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative, PDB code: 4phb was solved by D.W.Close, S.D'angelo, A.R.M.Bradbury, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.51 / 2.18
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 68.810, 122.840, 34.510, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 23.4

Gadolinium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Gadolinium atom in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative (pdb code 4phb). This binding sites where shown within 5.0 Angstroms radius around Gadolinium atom.
In total 12 binding sites of Gadolinium where determined in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative, PDB code: 4phb:
Jump to Gadolinium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Gadolinium binding site 1 out of 12 in 4phb

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Gadolinium binding site 1 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 1 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd401

b:30.5
occ:0.84
 OD2 A:ASP154 2.7 22.7 1.0
OD2 A:ASP178 2.7 24.2 1.0
O A:HOH627 2.8 27.5 1.0
O A:HOH601 2.8 21.1 1.0
OD1 A:ASP154 2.8 21.1 1.0
O A:HOH629 2.8 27.7 1.0
O A:HOH604 2.9 22.1 1.0
O A:HOH547 2.9 41.1 1.0
CG A:ASP154 3.1 21.8 1.0
HZ1 A:LYS227 3.7 29.5 1.0
HB2 A:ASP178 3.7 27.9 1.0
HB3 A:ASN177 3.8 28.9 1.0
CG A:ASP178 3.8 23.2 1.0
HZ2 A:LYS227 4.1 29.5 1.0
H A:ASP178 4.2 26.8 1.0
CB A:ASP178 4.3 23.3 1.0
O A:HOH570 4.3 28.5 1.0
NZ A:LYS227 4.4 24.6 1.0
O A:HOH654 4.5 34.7 1.0
CB A:ASP154 4.6 21.0 1.0
O A:HOH617 4.6 24.6 1.0
CB A:ASN177 4.7 24.1 1.0
O A:HOH606 4.7 23.0 1.0
HB2 A:ASP154 4.8 25.2 1.0
N A:ASP178 4.8 22.4 1.0
HB2 A:ASN177 4.9 28.9 1.0
OD1 A:ASP178 4.9 22.0 1.0
HE3 A:LYS227 4.9 32.6 1.0
O A:HOH626 4.9 27.5 1.0
HZ3 A:LYS227 5.0 29.5 1.0

Gadolinium binding site 2 out of 12 in 4phb

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Gadolinium binding site 2 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 2 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd402

b:39.2
occ:1.00
 OD2 A:ASP215 2.7 19.6 1.0
OD1 A:ASP215 2.7 22.2 1.0
OD2 A:ASP247 2.7 32.7 1.0
OD2 A:ASP244 2.8 31.0 1.0
O A:HOH639 2.8 30.6 1.0
O A:HOH665 2.8 38.0 1.0
O A:HOH612 2.9 24.2 1.0
OD2 A:ASP243 3.0 37.7 1.0
CG A:ASP215 3.0 21.4 1.0
CG A:ASP243 3.4 34.0 1.0
HB2 A:ASP247 3.6 31.3 1.0
H A:ASP244 3.7 31.9 1.0
HB2 A:ASP244 3.7 30.0 1.0
CG A:ASP247 3.7 30.0 1.0
CG A:ASP244 3.8 28.1 1.0
HD3 A:LYS269 3.8 43.0 1.0
OD1 A:ASP243 3.8 32.5 1.0
HB3 A:ASP243 3.8 37.8 1.0
O A:HOH669 3.9 38.9 1.0
HZ3 A:LYS269 4.1 51.6 1.0
CB A:ASP247 4.1 26.1 1.0
CB A:ASP243 4.2 31.5 1.0
HE3 A:LYS218 4.2 28.7 1.0
HB3 A:ASP247 4.3 31.3 1.0
CB A:ASP244 4.3 25.0 1.0
O A:HOH613 4.4 24.2 1.0
N A:ASP244 4.4 26.5 1.0
CB A:ASP215 4.5 19.7 1.0
CD A:LYS269 4.6 35.8 1.0
O A:HOH661 4.6 36.5 1.0
HD2 A:LYS269 4.6 43.0 1.0
HB2 A:ASP243 4.7 37.8 1.0
OD1 A:ASP244 4.8 27.9 1.0
OD1 A:ASP247 4.8 28.8 1.0
HZ2 A:LYS218 4.8 31.1 1.0
NZ A:LYS269 4.8 43.0 1.0
O A:HOH662 4.8 37.0 1.0
HZ2 A:LYS269 4.8 51.6 1.0
HB2 A:ASP215 4.9 23.7 1.0
HB3 A:ASP215 4.9 23.7 1.0

Gadolinium binding site 3 out of 12 in 4phb

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Gadolinium binding site 3 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 3 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd403

b:49.4
occ:1.00
 OD2 A:ASP142 2.7 24.8 1.0
O A:HOH511 2.8 33.1 1.0
OD1 A:ASP142 2.9 26.7 1.0
O A:HOH564 2.9 27.5 1.0
OD2 A:ASP139 3.0 28.9 1.0
CG A:ASP142 3.2 25.2 1.0
HB2 A:ASP139 3.4 37.2 1.0
O A:HOH673 3.5 40.3 1.0
CG A:ASP139 3.7 30.1 1.0
HB3 A:ASP139 3.9 37.2 1.0
CB A:ASP139 3.9 31.0 1.0
O A:HOH506 4.4 29.3 1.0
CB A:ASP142 4.6 24.9 1.0
O A:HOH636 4.7 29.1 1.0
O A:HOH622 4.8 26.9 1.0
OD1 A:ASP139 4.8 30.7 1.0
O A:HOH631 4.9 28.0 1.0
HB3 A:ASP142 4.9 29.8 1.0
O A:HOH568 4.9 37.9 1.0

Gadolinium binding site 4 out of 12 in 4phb

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Gadolinium binding site 4 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 4 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd404

b:30.6
occ:0.55
 OD1 A:ASN177 2.7 24.4 1.0
OD2 A:ASP153 2.7 29.4 1.0
O A:ARG152 2.8 31.0 1.0
O A:HOH565 2.8 27.5 1.0
HA A:ASP153 3.3 29.6 1.0
CG A:ASP153 3.4 26.9 1.0
HD21 A:ASN177 3.4 28.8 1.0
CG A:ASN177 3.6 24.3 1.0
C A:ARG152 3.8 31.1 1.0
ND2 A:ASN177 3.9 24.0 1.0
HG A:SER176 3.9 28.2 1.0
OD1 A:ASP153 4.0 26.4 1.0
CA A:ASP153 4.0 24.7 1.0
CB A:ASP153 4.3 25.0 1.0
HB3 A:ARG152 4.4 36.3 1.0
N A:ASP153 4.4 23.9 1.0
O A:HOH545 4.4 26.0 1.0
OG A:SER176 4.6 23.6 1.0
HB3 A:ASP153 4.6 30.0 1.0
O A:HOH617 4.7 24.6 1.0
HD22 A:ASN177 4.8 28.8 1.0
O A:HOH549 4.9 22.7 1.0
O A:HOH570 4.9 28.5 1.0
CA A:ARG152 5.0 30.5 1.0
HG2 A:LYS88 5.0 56.1 1.0
CB A:ASN177 5.0 24.1 1.0

Gadolinium binding site 5 out of 12 in 4phb

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Gadolinium binding site 5 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 5 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd405

b:44.8
occ:0.71
 OD1 A:ASP139 2.7 30.7 1.0
OE1 A:GLU138 2.8 28.8 1.0
O A:HOH506 2.9 29.3 1.0
OE2 A:GLU138 2.9 30.0 1.0
O A:HOH532 3.0 41.0 1.0
CD A:GLU138 3.2 29.1 1.0
CG A:ASP139 3.5 30.1 1.0
OD2 A:ASP139 3.6 28.9 1.0
O A:GLU138 4.4 32.4 1.0
O A:HOH569 4.4 40.6 1.0
O A:HOH622 4.5 26.9 1.0
HA A:ASP139 4.5 37.5 1.0
O A:HOH511 4.7 33.1 1.0
CG A:GLU138 4.7 28.5 1.0
C A:GLU138 4.7 31.5 1.0
CB A:ASP139 4.7 31.0 1.0
N A:ASP139 4.8 29.8 1.0
CA A:ASP139 4.9 31.3 1.0
HB3 A:GLU138 5.0 34.0 1.0

Gadolinium binding site 6 out of 12 in 4phb

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Gadolinium binding site 6 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 6 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd406

b:70.9
occ:0.77
 OE2 A:GLU60 2.8 43.5 1.0
OE1 A:GLU60 2.8 42.2 1.0
O A:HOH567 3.0 36.4 1.0
CD A:GLU60 3.1 42.4 1.0
O A:HOH576 4.0 30.7 1.0
HD2 A:ARG61 4.4 33.4 1.0
CG A:GLU60 4.7 40.6 1.0
O A:HOH556 4.7 39.0 1.0

Gadolinium binding site 7 out of 12 in 4phb

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Gadolinium binding site 7 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 7 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd407

b:0.6
occ:1.00
 OD1 A:ASN160 2.8 37.9 1.0
O A:HOH539 3.0 27.5 1.0
O A:HOH516 3.4 36.0 1.0
CG A:ASN160 4.0 38.3 1.0
HA A:ASN160 4.2 43.4 1.0
O A:HOH577 4.3 27.5 1.0
HA3 A:GLY183 4.5 23.8 1.0
HD21 A:ASN160 4.6 47.8 1.0
O A:GLY159 4.7 23.0 1.0
O A:HOH553 4.7 7.9 1.0
ND2 A:ASN160 4.8 39.8 1.0
CA A:ASN160 4.8 36.2 1.0
C A:GLY159 4.9 23.2 1.0
N A:ASN160 5.0 35.9 1.0
CB A:ASN160 5.0 37.7 1.0

Gadolinium binding site 8 out of 12 in 4phb

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Gadolinium binding site 8 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 8 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd408

b:0.7
occ:0.91
 O A:HOH628 2.7 27.5 1.0
OE2 A:GLU115 2.8 33.3 1.0
OE1 A:GLU115 2.8 32.9 1.0
CD A:GLU115 3.1 32.6 1.0
O A:HOH697 3.7 45.8 1.0
O A:GLU89 3.9 40.8 1.0
OE2 A:GLU91 4.3 34.3 1.0
HG3 A:GLU91 4.5 39.4 1.0
CG A:GLU115 4.6 30.8 1.0
HG3 A:GLU115 4.9 37.0 1.0
C A:GLU89 4.9 40.0 1.0
CD A:GLU91 5.0 33.9 1.0
HA A:GLU89 5.0 48.6 1.0

Gadolinium binding site 9 out of 12 in 4phb

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Gadolinium binding site 9 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 9 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd409

b:0.7
occ:0.52
 OE1 A:GLU136 2.9 33.1 1.0
OE2 A:GLU136 3.0 30.1 1.0
CD A:GLU136 3.3 31.3 1.0
HE2 A:LYS105 4.0 43.0 1.0
CG A:GLU136 4.8 30.1 1.0
CE A:LYS105 5.0 35.9 1.0

Gadolinium binding site 10 out of 12 in 4phb

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Gadolinium binding site 10 out of 12 in the Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative


Mono view


Stereo pair view

A full contact list of Gadolinium with other atoms in the Gd binding site number 10 of Structure of the Polysaccharide Lyase-Like Protein CTHE_2159 From C. Thermocellum, Gadolinium Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Gd410

b:47.8
occ:0.21
 OD1 A:ASP123 2.8 32.4 1.0
OD2 A:ASP123 3.4 32.4 1.0
HB3 A:ASN160 3.4 45.3 1.0
CG A:ASP123 3.5 31.8 1.0
CB A:ASN160 4.2 37.7 1.0
HD22 A:ASN160 4.2 47.8 1.0
HB2 A:ASN160 4.3 45.3 1.0
O A:HOH538 4.3 24.0 1.0
ND2 A:ASN160 4.5 39.8 1.0
CG A:ASN160 4.6 38.3 1.0
HA A:ASP123 4.9 35.7 1.0
CB A:ASP123 4.9 30.1 1.0

Reference:

D.W.Close, S.D'angelo, A.R.Bradbury. A New Family of Beta-Helix Proteins with Similarities to the Polysaccharide Lyases. Acta Crystallogr.,Sect.D V. 70 2583 2014.
ISSN: ESSN 1399-0047
PubMed: 25286843
DOI: 10.1107/S1399004714015934
Page generated: Sun Dec 13 19:00:00 2020

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