Calcium in PDB 4kjk: Room Temperature Wt Dhfr
Enzymatic activity of Room Temperature Wt Dhfr
All present enzymatic activity of Room Temperature Wt Dhfr:
1.5.1.3;
Protein crystallography data
The structure of Room Temperature Wt Dhfr, PDB code: 4kjk
was solved by
H.Van Den Bedem,
G.Bhabha,
K.Yang,
P.E.Wright,
J.S.Fraser,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
41.34 /
1.35
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
34.320,
45.510,
98.910,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
12.9 /
16.5
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Room Temperature Wt Dhfr
(pdb code 4kjk). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Room Temperature Wt Dhfr, PDB code: 4kjk:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 4kjk
Go back to
Calcium Binding Sites List in 4kjk
Calcium binding site 1 out
of 2 in the Room Temperature Wt Dhfr
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Room Temperature Wt Dhfr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca202
b:12.3
occ:1.00
|
O
|
A:HOH310
|
2.4
|
17.9
|
1.0
|
|
O
|
A:HOH311
|
2.4
|
20.1
|
1.0
|
|
OE2
|
A:GLU101
|
4.0
|
22.9
|
0.4
|
|
OE1
|
A:GLU101
|
4.6
|
19.5
|
0.4
|
|
OE1
|
A:GLU101
|
4.6
|
12.7
|
0.3
|
|
O
|
A:HOH410
|
4.7
|
19.9
|
1.0
|
|
CD
|
A:GLU101
|
4.8
|
19.7
|
0.4
|
|
OE1
|
A:GLU101
|
4.8
|
15.7
|
0.3
|
|
Calcium binding site 2 out
of 2 in 4kjk
Go back to
Calcium Binding Sites List in 4kjk
Calcium binding site 2 out
of 2 in the Room Temperature Wt Dhfr
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Room Temperature Wt Dhfr within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca203
b:38.5
occ:1.00
|
H
|
A:VAL119
|
1.9
|
16.4
|
0.6
|
|
H
|
A:VAL119
|
2.1
|
16.4
|
0.2
|
|
HB
|
A:VAL10
|
2.4
|
12.0
|
0.2
|
|
H
|
A:VAL119
|
2.5
|
16.4
|
0.2
|
|
O
|
A:VAL119
|
2.6
|
15.4
|
0.2
|
|
O
|
A:VAL10
|
2.7
|
10.2
|
0.6
|
|
HG12
|
A:VAL10
|
2.7
|
13.9
|
0.1
|
|
O
|
A:VAL10
|
2.8
|
10.6
|
0.1
|
|
O
|
A:VAL119
|
2.8
|
15.3
|
0.6
|
|
HG21
|
A:VAL13
|
2.8
|
7.7
|
0.2
|
|
HB
|
A:VAL10
|
2.8
|
12.0
|
0.1
|
|
O
|
A:VAL10
|
2.8
|
10.2
|
0.2
|
|
HB
|
A:VAL10
|
2.8
|
12.0
|
0.6
|
|
N
|
A:VAL119
|
2.9
|
13.0
|
0.6
|
|
O
|
A:HOH449
|
2.9
|
39.8
|
1.0
|
|
HG21
|
A:VAL13
|
3.0
|
7.7
|
0.4
|
|
HA
|
A:GLU118
|
3.0
|
15.8
|
0.2
|
|
N
|
A:VAL119
|
3.1
|
16.4
|
0.2
|
|
O
|
A:VAL119
|
3.1
|
15.5
|
0.2
|
|
N
|
A:VAL119
|
3.1
|
14.9
|
0.2
|
|
HA
|
A:GLU118
|
3.1
|
15.8
|
0.6
|
|
HB
|
A:VAL119
|
3.2
|
17.3
|
0.6
|
|
HA
|
A:GLU118
|
3.2
|
15.8
|
0.2
|
|
HB
|
A:VAL13
|
3.2
|
7.9
|
0.4
|
|
HB
|
A:VAL13
|
3.3
|
7.9
|
0.2
|
|
CB
|
A:VAL10
|
3.3
|
13.9
|
0.2
|
|
H
|
A:VAL10
|
3.4
|
8.7
|
0.2
|
|
HG23
|
A:VAL13
|
3.4
|
7.7
|
0.2
|
|
HB
|
A:VAL13
|
3.4
|
7.9
|
0.4
|
|
HG21
|
A:VAL13
|
3.4
|
7.7
|
0.4
|
|
H
|
A:VAL10
|
3.4
|
8.7
|
0.1
|
|
CB
|
A:VAL10
|
3.5
|
11.2
|
0.1
|
|
CG1
|
A:VAL10
|
3.5
|
11.4
|
0.1
|
|
HG23
|
A:VAL13
|
3.5
|
7.7
|
0.4
|
|
C
|
A:VAL10
|
3.5
|
10.4
|
0.1
|
|
CG2
|
A:VAL13
|
3.5
|
10.6
|
0.2
|
|
C
|
A:VAL10
|
3.5
|
10.7
|
0.2
|
|
C
|
A:VAL10
|
3.5
|
9.5
|
0.6
|
|
C
|
A:VAL119
|
3.5
|
15.8
|
0.2
|
|
HG12
|
A:VAL10
|
3.5
|
13.9
|
0.2
|
|
C
|
A:VAL119
|
3.5
|
15.6
|
0.6
|
|
HB1
|
A:ALA9
|
3.6
|
8.3
|
0.1
|
|
CG2
|
A:VAL13
|
3.6
|
7.7
|
0.4
|
|
HB2
|
A:ASP11
|
3.6
|
11.0
|
0.3
|
|
HB2
|
A:ASP11
|
3.6
|
11.0
|
0.6
|
|
CA
|
A:VAL119
|
3.7
|
14.5
|
0.6
|
|
N
|
A:VAL10
|
3.7
|
11.3
|
0.2
|
|
N
|
A:VAL10
|
3.7
|
9.6
|
0.1
|
|
CA
|
A:VAL10
|
3.7
|
12.3
|
0.2
|
|
C
|
A:VAL119
|
3.7
|
16.1
|
0.2
|
|
HB
|
A:VAL119
|
3.7
|
17.3
|
0.2
|
|
CA
|
A:VAL10
|
3.7
|
10.6
|
0.1
|
|
CB
|
A:VAL10
|
3.7
|
12.0
|
0.6
|
|
HG12
|
A:VAL10
|
3.7
|
13.9
|
0.6
|
|
HB3
|
A:ALA9
|
3.8
|
8.3
|
0.2
|
|
H
|
A:VAL10
|
3.8
|
8.7
|
0.6
|
|
O
|
A:ALA117
|
3.8
|
10.8
|
0.2
|
|
CA
|
A:VAL119
|
3.8
|
15.9
|
0.2
|
|
C
|
A:GLU118
|
3.8
|
14.0
|
0.2
|
|
HG23
|
A:VAL13
|
3.8
|
7.7
|
0.4
|
|
HG11
|
A:VAL10
|
3.8
|
13.9
|
0.1
|
|
HB3
|
A:ALA9
|
3.8
|
8.3
|
0.1
|
|
HB1
|
A:ALA9
|
3.9
|
8.3
|
0.2
|
|
CA
|
A:GLU118
|
3.9
|
15.8
|
0.2
|
|
N
|
A:VAL10
|
3.9
|
8.7
|
0.6
|
|
CA
|
A:VAL119
|
3.9
|
16.5
|
0.2
|
|
CA
|
A:VAL10
|
3.9
|
10.5
|
0.6
|
|
C
|
A:GLU118
|
3.9
|
10.7
|
0.6
|
|
CB
|
A:VAL13
|
3.9
|
10.4
|
0.2
|
|
CG1
|
A:VAL10
|
3.9
|
14.8
|
0.2
|
|
CG2
|
A:VAL13
|
3.9
|
8.2
|
0.4
|
|
CB
|
A:VAL119
|
3.9
|
14.5
|
0.6
|
|
C
|
A:GLU118
|
3.9
|
16.1
|
0.2
|
|
HB
|
A:VAL119
|
4.0
|
17.3
|
0.2
|
|
CA
|
A:GLU118
|
4.0
|
10.3
|
0.6
|
|
O
|
A:ALA117
|
4.0
|
8.9
|
0.6
|
|
CB
|
A:VAL13
|
4.0
|
7.9
|
0.4
|
|
CA
|
A:GLU118
|
4.0
|
13.6
|
0.2
|
|
CB
|
A:VAL13
|
4.0
|
7.6
|
0.4
|
|
HB1
|
A:ALA9
|
4.1
|
8.3
|
0.6
|
|
HB3
|
A:ALA9
|
4.1
|
8.3
|
0.6
|
|
HG11
|
A:VAL13
|
4.1
|
8.5
|
0.2
|
|
O
|
A:ALA117
|
4.2
|
13.8
|
0.2
|
|
HG11
|
A:VAL10
|
4.2
|
13.9
|
0.2
|
|
CB
|
A:ALA9
|
4.2
|
7.8
|
0.1
|
|
CG1
|
A:VAL10
|
4.3
|
13.9
|
0.6
|
|
HG11
|
A:VAL13
|
4.3
|
8.5
|
0.4
|
|
HG11
|
A:VAL13
|
4.3
|
8.5
|
0.4
|
|
HG23
|
A:VAL119
|
4.3
|
17.1
|
0.6
|
|
CB
|
A:ALA9
|
4.3
|
9.7
|
0.2
|
|
H
|
A:VAL13
|
4.3
|
7.7
|
0.4
|
|
H
|
A:VAL13
|
4.3
|
7.7
|
0.2
|
|
CB
|
A:VAL119
|
4.4
|
17.3
|
0.2
|
|
HG13
|
A:VAL10
|
4.4
|
13.9
|
0.1
|
|
HB3
|
A:GLU118
|
4.4
|
17.7
|
0.2
|
|
H
|
A:VAL13
|
4.4
|
7.7
|
0.4
|
|
HG22
|
A:VAL13
|
4.5
|
7.7
|
0.2
|
|
CB
|
A:VAL119
|
4.5
|
17.8
|
0.2
|
|
CG2
|
A:VAL10
|
4.5
|
14.8
|
0.2
|
|
C
|
A:ALA9
|
4.5
|
8.9
|
0.1
|
|
C
|
A:ALA9
|
4.5
|
10.8
|
0.2
|
|
C
|
A:ALA9
|
4.6
|
8.1
|
0.6
|
|
CB
|
A:ALA9
|
4.6
|
8.3
|
0.6
|
|
HG23
|
A:VAL10
|
4.6
|
12.0
|
0.2
|
|
N
|
A:ASP11
|
4.6
|
10.7
|
1.0
|
|
HG22
|
A:VAL13
|
4.6
|
7.7
|
0.4
|
|
HG3
|
A:GLU118
|
4.6
|
19.3
|
0.2
|
|
HG11
|
A:VAL10
|
4.6
|
13.9
|
0.6
|
|
CG1
|
A:VAL13
|
4.6
|
10.4
|
0.2
|
|
CB
|
A:ASP11
|
4.6
|
11.5
|
0.6
|
|
HB3
|
A:GLU118
|
4.7
|
17.7
|
0.6
|
|
CB
|
A:GLU118
|
4.7
|
17.7
|
0.2
|
|
HA
|
A:VAL119
|
4.7
|
16.5
|
0.6
|
|
CB
|
A:ASP11
|
4.7
|
11.0
|
0.3
|
|
HA
|
A:VAL119
|
4.7
|
16.5
|
0.2
|
|
C
|
A:ALA117
|
4.7
|
10.5
|
0.2
|
|
CG2
|
A:VAL119
|
4.7
|
14.7
|
0.6
|
|
CG1
|
A:VAL13
|
4.7
|
6.9
|
0.4
|
|
N
|
A:GLU120
|
4.8
|
15.9
|
1.0
|
|
CG1
|
A:VAL13
|
4.8
|
8.5
|
0.4
|
|
HG12
|
A:VAL119
|
4.8
|
17.7
|
0.2
|
|
HA
|
A:VAL10
|
4.8
|
10.5
|
0.2
|
|
HG21
|
A:VAL10
|
4.8
|
12.0
|
0.2
|
|
O
|
A:GLU118
|
4.8
|
14.8
|
0.2
|
|
HA
|
A:VAL10
|
4.8
|
10.5
|
0.1
|
|
OD2
|
A:ASP11
|
4.8
|
16.4
|
0.6
|
|
HA
|
A:VAL119
|
4.9
|
16.5
|
0.2
|
|
C
|
A:ALA117
|
4.9
|
7.5
|
0.6
|
|
N
|
A:GLU118
|
4.9
|
11.7
|
0.2
|
|
CG2
|
A:VAL10
|
4.9
|
11.7
|
0.1
|
|
N
|
A:GLU118
|
4.9
|
14.5
|
0.2
|
|
N
|
A:GLU118
|
4.9
|
8.5
|
0.6
|
|
HG13
|
A:VAL10
|
4.9
|
13.9
|
0.2
|
|
C
|
A:ALA117
|
4.9
|
13.7
|
0.2
|
|
HG12
|
A:VAL119
|
5.0
|
17.7
|
0.2
|
|
HA
|
A:VAL10
|
5.0
|
10.5
|
0.6
|
|
HG3
|
A:GLU118
|
5.0
|
19.3
|
0.2
|
|
HG12
|
A:VAL119
|
5.0
|
17.7
|
0.6
|
|
HG22
|
A:VAL13
|
5.0
|
7.7
|
0.4
|
|
CB
|
A:GLU118
|
5.0
|
14.4
|
0.6
|
|
Reference:
H.Van Den Bedem,
G.Bhabha,
K.Yang,
P.E.Wright,
J.S.Fraser.
Automated Identification of Functional Dynamic Contact Networks From X-Ray Crystallography. Nat.Methods V. 10 896 2013.
ISSN: ISSN 1548-7091
PubMed: 23913260
DOI: 10.1038/NMETH.2592
Page generated: Sun Jul 14 09:08:18 2024
|
