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Chlorine in PDB 2jkv: Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A

Enzymatic activity of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A

All present enzymatic activity of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A:
1.1.1.44;

Protein crystallography data

The structure of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A, PDB code: 2jkv was solved by E.S.Pilka, K.L.Kavanagh, F.Von Delft, J.R.C.Muniz, J.Murray, S.Picaud, K.Guo, A.Edwards, C.H.Arrowsmith, J.Weigelt, C.Bountra, U.Oppermann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.90 / 2.53
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.643, 204.714, 170.319, 90.00, 90.65, 90.00
R / Rfree (%) 15.6 / 20.7

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A (pdb code 2jkv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 11 binding sites of Chlorine where determined in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A, PDB code: 2jkv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 11 in 2jkv

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Chlorine binding site 1 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1484

b:37.9
occ:1.00
 O A:HOH2261 3.1 18.9 1.0
NZ A:LYS184 3.1 19.3 1.0
O A:HOH2260 3.2 30.8 1.0
ND2 A:ASN188 3.3 27.7 1.0
ND2 A:ASN103 3.3 32.6 1.0
O B:HOH2265 3.4 30.6 1.0
O A:HOH2080 3.5 27.0 1.0
C4N B:NAP500 3.6 32.7 1.0
C5N B:NAP500 3.6 28.9 1.0
OD1 A:ASN188 3.9 32.6 1.0
CE A:LYS184 4.0 21.8 1.0
CG A:ASN188 4.0 29.0 1.0
C3N B:NAP500 4.1 39.1 1.0
OD1 A:ASN103 4.1 24.6 1.0
CG A:ASN103 4.2 25.8 1.0
C6N B:NAP500 4.2 26.1 1.0
O2 A:SO41485 4.5 18.9 1.0
C2N B:NAP500 4.6 32.4 1.0
N1N B:NAP500 4.6 33.9 1.0
O A:VAL128 4.9 27.6 1.0
O B:HOH2264 5.0 26.0 1.0

Chlorine binding site 2 out of 11 in 2jkv

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Chlorine binding site 2 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1487

b:80.7
occ:1.00
 O A:HOH2096 2.7 38.0 1.0
NZ A:LYS154 3.2 56.6 1.0
NE1 A:TRP150 3.3 33.9 1.0
OD1 A:ASP172 3.5 50.9 1.0
CE A:LYS154 3.6 54.8 1.0
O A:HOH2104 4.0 45.9 1.0
CD A:LYS154 4.1 46.2 1.0
CD1 A:TRP150 4.2 28.9 1.0
CE2 A:TRP150 4.3 29.1 1.0
CG A:ASP172 4.6 57.9 1.0
CZ2 A:TRP150 4.6 24.5 1.0
OD2 A:ASP172 4.8 78.3 1.0
NE2 A:GLN158 5.0 31.5 1.0

Chlorine binding site 3 out of 11 in 2jkv

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Chlorine binding site 3 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1488

b:62.7
occ:1.00
 CE A:LYS303 3.4 72.2 1.0
NZ A:LYS303 4.2 76.4 1.0
CG A:LYS303 4.4 57.0 1.0
CD A:LYS303 4.5 55.6 1.0
O A:HOH2170 4.6 43.7 1.0
CB A:LYS303 4.9 30.9 1.0

Chlorine binding site 4 out of 11 in 2jkv

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Chlorine binding site 4 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1484

b:34.0
occ:1.00
 NZ B:LYS184 3.1 26.0 1.0
O B:HOH2266 3.1 30.6 1.0
ND2 B:ASN103 3.1 27.1 1.0
O B:HOH2268 3.2 16.9 1.0
ND2 B:ASN188 3.3 35.6 1.0
O A:HOH2257 3.3 31.4 1.0
C4N A:NAP500 3.6 33.2 1.0
C5N A:NAP500 3.7 29.3 1.0
OD1 B:ASN188 3.9 36.8 1.0
CE B:LYS184 4.0 21.8 1.0
CG B:ASN188 4.0 26.4 1.0
C3N A:NAP500 4.0 36.5 1.0
CG B:ASN103 4.1 24.9 1.0
OD1 B:ASN103 4.1 24.2 1.0
C6N A:NAP500 4.3 29.9 1.0
O1 B:SO41486 4.5 19.1 1.0
C2N A:NAP500 4.6 25.2 1.0
N1N A:NAP500 4.7 29.4 1.0
O A:HOH2255 4.8 16.9 1.0
O B:VAL128 4.9 24.8 1.0
C7N A:NAP500 4.9 27.3 1.0

Chlorine binding site 5 out of 11 in 2jkv

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Chlorine binding site 5 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1485

b:57.0
occ:1.00
 NZ B:LYS154 3.5 54.6 1.0
NE1 B:TRP150 3.6 34.4 1.0
CE B:LYS154 3.9 57.2 1.0
CD1 B:TRP150 4.3 24.9 1.0
OD1 B:ASP172 4.3 54.7 1.0
CD B:LYS154 4.6 43.9 1.0
CE2 B:TRP150 4.7 21.5 1.0

Chlorine binding site 6 out of 11 in 2jkv

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Chlorine binding site 6 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1488

b:61.1
occ:1.00
 O B:HOH2174 2.9 53.0 1.0
CE B:LYS303 3.6 72.5 1.0
NZ B:LYS303 4.0 73.3 1.0
NZ A:LYS396 4.5 67.7 1.0
CG B:LYS303 4.8 55.6 1.0
CD B:LYS303 4.8 60.0 1.0
CE A:LYS396 4.9 70.5 1.0

Chlorine binding site 7 out of 11 in 2jkv

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Chlorine binding site 7 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1486

b:81.1
occ:1.00
 O D:HOH2112 3.0 15.4 1.0
NZ D:LYS184 3.3 35.3 1.0
OG D:SER129 3.6 42.7 1.0
C4N C:NAP500 3.6 41.4 1.0
CG1 D:ILE367 3.6 40.0 1.0
C5N C:NAP500 3.8 41.0 1.0
N D:GLY130 3.9 38.3 1.0
CA D:SER129 3.9 34.4 1.0
OE1 D:GLU191 4.1 32.4 1.0
O D:VAL128 4.1 29.7 1.0
N D:GLY131 4.2 26.6 1.0
CB D:SER129 4.3 45.6 1.0
CE1 D:HIS187 4.3 34.2 1.0
CD1 D:ILE367 4.4 27.5 1.0
C D:SER129 4.4 36.4 1.0
CE D:LYS184 4.5 25.2 1.0
OD1 D:ASN188 4.7 43.1 1.0
C3N C:NAP500 4.7 43.5 1.0
CB D:ILE367 4.9 30.2 1.0
O7N C:NAP500 4.9 42.1 1.0
CA D:GLY131 4.9 21.7 1.0
N D:SER129 5.0 27.1 1.0
C D:VAL128 5.0 27.2 1.0
ND1 D:HIS187 5.0 25.6 1.0
CA D:GLY130 5.0 28.7 1.0

Chlorine binding site 8 out of 11 in 2jkv

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Chlorine binding site 8 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1486

b:67.9
occ:1.00
 NE1 E:TRP150 3.4 33.2 1.0
CD1 E:TRP150 3.8 27.7 1.0
CE E:LYS154 3.8 57.7 1.0
O E:HOH2029 4.2 43.0 1.0
NZ E:LYS154 4.7 56.2 1.0
CE2 E:TRP150 4.7 23.2 1.0
OD1 E:ASP172 4.8 50.8 1.0
NZ E:LYS147 4.8 48.7 1.0
CD E:LYS154 4.9 48.5 1.0
CE E:LYS147 5.0 38.9 1.0

Chlorine binding site 9 out of 11 in 2jkv

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Chlorine binding site 9 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1488

b:75.2
occ:1.00
 NZ F:LYS396 3.3 68.2 1.0
CE E:LYS303 3.8 72.5 1.0
NZ E:LYS303 4.1 77.0 1.0
CD E:LYS303 4.5 56.8 1.0
CG E:LYS303 4.5 54.1 1.0
CE F:LYS396 4.7 69.7 1.0

Chlorine binding site 10 out of 11 in 2jkv

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Chlorine binding site 10 out of 11 in the Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1473

b:35.1
occ:1.00
 O F:HOH2247 3.1 13.9 1.0
O F:HOH2128 3.1 28.6 1.0
ND2 F:ASN103 3.2 30.0 1.0
NZ F:LYS184 3.3 22.4 1.0
O E:HOH2235 3.4 26.0 1.0
ND2 F:ASN188 3.5 44.1 1.0
O F:HOH2090 3.5 15.8 1.0
C4N E:NAP500 3.5 24.1 1.0
C5N E:NAP500 3.7 34.2 1.0
OD1 F:ASN188 4.0 27.9 1.0
C3N E:NAP500 4.0 28.4 1.0
CE F:LYS184 4.0 12.5 1.0
CG F:ASN188 4.1 27.4 1.0
CG F:ASN103 4.2 23.3 1.0
C6N E:NAP500 4.2 27.0 1.0
OD1 F:ASN103 4.3 21.0 1.0
O1 F:SO41474 4.4 19.1 1.0
C2N E:NAP500 4.5 28.1 1.0
N1N E:NAP500 4.6 30.7 1.0
C7N E:NAP500 4.9 22.9 1.0
O F:VAL128 4.9 30.3 1.0

Reference:

S.S.Ng, F.Von Delft, E.S.Pilka, K.L.Kavanagh, M.A.Mcdonough, P.Savitsky, C.H.Arrowsmith, J.Weigelt, A.Edwards, M.Sundstrom, C.J.Schofield, U.Oppermann. Structure of Human Phosphogluconate Dehydrogenase in Complex with Nadph at 2.53A To Be Published.
Page generated: Sat Jul 20 09:01:13 2024

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