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Calcium in PDB 4kak: Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006)

Enzymatic activity of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006)

All present enzymatic activity of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006):
1.5.1.3;

Protein crystallography data

The structure of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006), PDB code: 4kak was solved by K.M.Lamb, A.C.Anderson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.08 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 88.077, 93.634, 96.039, 90.00, 90.00, 90.00
R / Rfree (%) 22.3 / 26.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006) (pdb code 4kak). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006), PDB code: 4kak:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4kak

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Calcium binding site 1 out of 4 in the Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca206

b:67.3
occ:1.00
 O A:HOH381 2.5 25.4 1.0
OG A:SER3 2.5 12.9 1.0
OD1 A:ASN5 2.8 6.9 1.0
O A:HOH438 2.8 14.2 1.0
CG A:ASN5 3.4 6.7 1.0
ND2 A:ASN5 3.4 7.9 1.0
CE A:LYS132 3.5 15.8 1.0
CB A:SER3 3.6 16.9 1.0
O A:HOH387 3.7 20.5 1.0
CE1 A:HIS130 3.9 5.3 1.0
ND1 A:HIS130 4.1 7.6 1.0
NZ A:LYS132 4.2 18.1 1.0
CE A:MET111 4.2 16.1 0.8
O A:LEU4 4.2 5.1 1.0
O A:HOH320 4.4 14.2 1.0
C A:LEU4 4.6 5.5 1.0
C A:SER3 4.6 10.9 1.0
N A:LEU4 4.7 7.2 1.0
CA A:SER3 4.7 14.0 1.0
CD A:LYS132 4.8 10.9 1.0
CB A:ASN5 4.8 4.3 1.0
CG A:LYS132 4.9 7.3 1.0
O A:SER3 5.0 14.8 1.0
CB A:LYS132 5.0 2.3 1.0

Calcium binding site 2 out of 4 in 4kak

Go back to Calcium Binding Sites List in 4kak
Calcium binding site 2 out of 4 in the Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca205

b:61.6
occ:1.00
 O B:HOH390 2.5 43.0 1.0
O B:HOH428 2.8 23.7 1.0
O B:HOH438 2.9 30.8 1.0
O B:ARG32 2.9 3.9 1.0
CB B:ARG32 3.4 9.7 1.0
CA B:ARG32 3.6 5.1 1.0
C B:ARG32 3.6 5.5 1.0
O B:HOH416 3.7 42.9 1.0
CG B:ARG32 3.9 15.3 1.0
N B:ARG36 3.9 6.0 1.0
CB B:GLN35 4.0 10.3 1.0
CB B:ARG36 4.1 6.2 1.0
CD B:ARG32 4.3 35.6 1.0
CA B:ARG36 4.4 6.5 1.0
O B:HOH325 4.6 14.3 1.0
C B:GLN35 4.6 6.8 1.0
O B:HOH459 4.7 31.8 1.0
N B:TYR33 4.8 1.9 1.0
CA B:GLN35 4.8 6.2 1.0
CG B:GLN35 5.0 14.5 1.0
N B:ARG32 5.0 7.2 1.0

Calcium binding site 3 out of 4 in 4kak

Go back to Calcium Binding Sites List in 4kak
Calcium binding site 3 out of 4 in the Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca206

b:34.4
occ:1.00
 O B:HOH317 2.6 10.6 1.0
O B:HOH380 2.6 26.3 1.0
O B:ILE138 2.9 3.2 1.0
CB B:ARG137 3.4 2.9 1.0
O B:VAL10 3.5 6.3 1.0
N B:ILE138 3.5 3.5 1.0
CA B:ARG137 3.5 2.4 1.0
C B:ARG137 3.6 2.5 1.0
C B:ILE138 3.6 4.2 1.0
CD B:ARG137 3.6 4.2 1.0
CA B:GLN12 3.7 10.6 1.0
N B:GLN12 3.7 4.0 1.0
C B:SER11 3.7 5.2 1.0
O B:SER11 3.7 6.3 1.0
O B:HOH384 4.1 34.4 1.0
CG B:ARG137 4.1 4.1 1.0
CA B:ILE138 4.2 3.5 1.0
O B:ARG137 4.3 3.4 1.0
N B:MET139 4.3 5.1 1.0
CB B:GLN12 4.4 11.1 1.0
CA B:MET139 4.5 7.6 1.0
C B:VAL10 4.5 6.1 1.0
CA B:SER11 4.5 3.9 1.0
CG B:GLN12 4.7 17.1 1.0
CG1 B:VAL10 4.8 5.4 0.5
C B:GLN12 4.8 10.9 1.0
O B:HOH337 4.9 36.1 1.0
NE B:ARG137 4.9 4.4 1.0
CG B:MET139 4.9 8.2 1.0
NH1 B:ARG137 4.9 8.6 1.0
N B:ARG137 4.9 2.0 1.0
N B:SER11 5.0 3.1 1.0

Calcium binding site 4 out of 4 in 4kak

Go back to Calcium Binding Sites List in 4kak
Calcium binding site 4 out of 4 in the Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Human Dihydrofolate Reductase Complexed with Nadph and 6-Ethyl-5-[(3S)-3-[3-Methoxy-5-(Pyridine-4-Yl)Phenyl]But-1- Yn-1-Yl]Pyrimidine-2,4-Diamine (UCP1006) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca207

b:49.8
occ:1.00
 O B:HOH388 2.5 18.8 1.0
O A:HOH383 2.6 24.3 1.0
OE1 B:GLU183 2.7 14.7 1.0
OH B:TYR162 3.2 23.8 1.0
CE1 B:TYR162 3.3 16.4 1.0
CB A:PRO25 3.4 16.0 0.5
CB A:PRO25 3.5 15.9 0.5
CG A:PRO25 3.5 13.6 0.5
CG A:PRO25 3.5 13.9 0.5
CD B:GLU183 3.6 13.1 1.0
CD A:LYS173 3.7 18.9 1.0
CZ B:TYR162 3.7 19.5 1.0
OE2 B:GLU183 3.8 19.9 1.0
CD B:LYS132 3.9 11.3 1.0
CB A:LYS173 4.0 10.4 1.0
CG A:LYS173 4.3 11.1 1.0
NZ B:LYS132 4.3 24.5 1.0
CD1 B:TYR162 4.4 22.0 1.0
NZ A:LYS173 4.5 19.7 1.0
CE B:LYS132 4.5 18.3 1.0
CD1 B:LEU159 4.5 8.2 1.0
CE A:LYS173 4.5 20.9 1.0
O A:LYS173 4.6 11.5 1.0
NE2 B:HIS130 4.6 7.2 1.0
CG B:LYS132 4.8 8.9 1.0
O A:HOH458 4.8 31.8 1.0
CG B:GLU183 4.9 12.7 1.0
CD A:PRO25 4.9 12.8 0.5
CD A:PRO25 4.9 12.8 0.5
CA A:PRO25 5.0 9.6 0.5

Reference:

K.M.Lamb, N.G-Dayanandan, D.L.Wright, A.C.Anderson. Elucidating Features That Drive the Design of Selective Antifolates Using Crystal Structures of Human Dihydrofolate Reductase. Biochemistry V. 52 7318 2013.
ISSN: ISSN 0006-2960
PubMed: 24053334
DOI: 10.1021/BI400852H
Page generated: Sun Jul 14 09:00:51 2024

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