Atomistry » Calcium » PDB 4k9m-4ko1 » 4kig
Atomistry »
  Calcium »
    PDB 4k9m-4ko1 »
      4kig »

Calcium in PDB 4kig: Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid

Protein crystallography data

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid, PDB code: 4kig was solved by Y.C.Liu, X.W.Zou, H.C.Chan, C.J.Huang, T.L.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.88 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.485, 81.145, 137.422, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 24.8

Other elements in 4kig:

The structure of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid (pdb code 4kig). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid, PDB code: 4kig:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 1 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


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 Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:49.2
occ:1.00
 O B:HOH668 2.9 20.1 1.0
CB B:PRO285 3.8 28.2 1.0
NH1 A:ARG12 3.8 43.6 1.0
O A:HOH628 3.9 44.2 1.0
CA B:PRO285 3.9 28.2 1.0
CB A:ARG11 4.0 35.1 1.0
O A:ARG11 4.2 28.1 1.0
C A:ARG11 4.3 30.1 1.0
CB A:ALA15 4.4 22.1 1.0
N A:ARG12 4.6 28.2 1.0
CD A:ARG11 4.6 38.8 1.0
CA A:ARG12 4.7 29.5 1.0
CZ A:ARG12 4.7 43.6 1.0
O A:HOH643 4.7 20.4 1.0
CA A:ARG11 4.8 32.3 1.0
CG A:ARG11 4.8 39.0 1.0
N B:PRO285 4.8 28.6 1.0
O B:LEU284 4.8 27.9 1.0
N B:VAL286 4.9 25.2 1.0
NE A:ARG11 5.0 43.9 1.0

Calcium binding site 2 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 2 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


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 Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:41.6
occ:1.00
 O B:HOH678 2.8 27.0 1.0
NH2 A:ARG109 3.3 25.8 1.0
CG B:GLU106 3.4 42.9 1.0
O B:HOH677 3.5 27.7 1.0
CZ A:ARG109 3.6 25.2 1.0
CB B:GLU106 3.7 34.2 1.0
C B:ARG127 3.7 28.1 1.0
N B:ASP128 3.7 26.2 1.0
NE2 B:GLN126 3.9 57.4 1.0
CB B:ASP128 3.9 27.5 1.0
NE A:ARG109 4.0 25.1 1.0
CG B:GLN126 4.0 45.2 1.0
CA B:ARG127 4.1 27.5 1.0
OE1 B:GLU106 4.1 60.8 1.0
O B:ARG127 4.1 28.0 1.0
CA B:ASP128 4.1 26.7 1.0
NH1 A:ARG109 4.2 25.9 1.0
CD B:GLU106 4.3 50.2 1.0
CD B:GLN126 4.4 53.8 1.0
N B:ARG127 4.5 30.6 1.0
O B:GLN126 4.6 31.6 1.0
C B:GLN126 4.7 33.4 1.0
OE2 A:GLU106 4.7 31.8 1.0
CG B:ASP128 4.9 29.8 1.0
CD A:ARG109 5.0 24.2 1.0
OE1 A:GLU106 5.0 33.1 1.0
CA B:GLU106 5.0 29.4 1.0

Calcium binding site 3 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 3 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


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 Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:49.3
occ:1.00
 CA A:PRO85 3.8 28.9 1.0
N A:PRO85 4.0 27.6 1.0
CB A:PRO85 4.2 29.5 1.0
C A:GLY84 4.3 25.9 1.0
CD A:PRO85 4.4 28.9 1.0
O A:GLY84 4.6 25.1 1.0
CG A:PRO85 4.8 29.4 1.0

Calcium binding site 4 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 4 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


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 Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:58.9
occ:1.00
 OD2 A:ASP309 2.6 33.1 1.0
OD1 A:ASP306 2.6 44.0 1.0
CG A:ASP309 3.4 28.1 1.0
CB A:ASP309 3.6 24.5 1.0
CG A:ASP306 3.8 38.5 1.0
O1 A:34H503 4.5 39.0 1.0
CA A:ASP306 4.5 28.4 1.0
OD1 A:ASP309 4.6 26.0 1.0
CB A:ASP306 4.6 32.6 1.0
OD2 A:ASP306 4.7 39.6 1.0
O2 A:34H503 4.7 46.7 1.0
C1 A:34H503 4.9 39.4 1.0

Calcium binding site 5 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 5 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca508

b:54.4
occ:1.00
 C A:LEU45 4.0 41.3 1.0
OG1 A:THR80 4.0 41.9 1.0
O A:LEU45 4.1 39.9 1.0
N A:ASP46 4.1 39.4 1.0
CD A:LYS44 4.2 60.6 1.0
CA A:LEU45 4.3 40.9 1.0
CB A:ASP46 4.4 43.2 1.0
O A:HOH681 4.4 30.6 1.0
CB A:LYS44 4.6 49.0 1.0
N A:LEU45 4.6 44.2 1.0
CA A:ASP46 4.7 39.8 1.0
CG A:LYS44 4.7 55.6 1.0
C A:LYS44 4.9 45.8 1.0

Calcium binding site 6 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 6 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca504

b:36.0
occ:1.00
 O B:HOH640 2.2 40.3 1.0
NH2 B:ARG109 3.5 34.3 1.0
CG A:GLU106 3.5 30.2 1.0
O A:HOH718 3.7 22.6 1.0
C A:ARG127 3.7 38.5 1.0
N A:ASP128 3.7 39.3 1.0
CB A:GLU106 3.8 26.4 1.0
CA A:ARG127 4.0 39.9 1.0
CZ B:ARG109 4.0 33.2 1.0
O B:HOH676 4.0 34.3 1.0
O A:ARG127 4.1 40.3 1.0
CG A:GLN126 4.1 60.9 1.0
CA A:ASP128 4.2 38.3 1.0
CB A:ASP128 4.2 38.1 1.0
N A:ARG127 4.4 41.0 1.0
NE B:ARG109 4.4 29.5 1.0
C A:GLN126 4.5 46.0 1.0
O A:GLN126 4.5 46.1 1.0
NH1 B:ARG109 4.7 32.2 1.0
CB A:GLN126 4.7 55.2 1.0
CD A:GLU106 4.9 29.3 1.0

Calcium binding site 7 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 7 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca505

b:28.1
occ:1.00
 CD B:LYS44 3.5 50.6 1.0
C B:LEU45 3.9 32.3 1.0
CG2 B:THR80 4.0 35.5 1.0
O B:LEU45 4.1 33.5 1.0
N B:ASP46 4.1 30.3 1.0
CA B:LEU45 4.3 32.8 1.0
N B:LEU45 4.4 33.0 1.0
CG B:LYS44 4.5 42.8 1.0
CE B:LYS44 4.5 55.6 1.0
CB B:ASP46 4.6 29.7 1.0
CA B:ASP46 4.6 29.6 1.0
CB B:LYS44 4.7 38.9 1.0
C B:LYS44 4.8 35.5 1.0
OG1 B:THR80 4.9 40.8 1.0

Calcium binding site 8 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 8 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca506

b:54.9
occ:1.00
 N B:GLY182 3.5 51.9 1.0
C B:PHE180 3.6 55.0 1.0
CA B:PHE180 3.8 54.4 1.0
CB B:PHE180 3.8 55.5 1.0
O B:PHE180 3.9 48.3 1.0
N B:PRO181 3.9 54.6 1.0
CA B:GLY182 4.0 51.8 1.0
CD B:PRO181 4.0 53.2 1.0
CD1 B:PHE180 4.3 58.7 1.0
C B:GLY182 4.5 48.2 1.0
CG B:PHE180 4.5 56.1 1.0
N B:VAL183 4.6 46.9 1.0
C B:PRO181 4.6 54.3 1.0
CG2 B:THR158 4.7 35.2 1.0
CA B:PRO181 4.8 54.5 1.0

Calcium binding site 9 out of 9 in 4kig

Go back to Calcium Binding Sites List in 4kig
Calcium binding site 9 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca507

b:56.8
occ:1.00
 NH1 B:ARG248 3.5 34.4 1.0
OE1 B:GLU249 3.8 62.4 1.0
CD B:GLU249 3.8 59.8 1.0
N B:GLU249 3.9 35.5 1.0
CA B:GLU249 3.9 38.4 1.0
CB B:GLU249 3.9 44.2 1.0
CG B:ARG248 4.0 30.6 1.0
OE2 B:GLU249 4.1 50.8 1.0
CD B:ARG248 4.2 29.2 1.0
CB B:ARG248 4.2 31.0 1.0
C B:ARG248 4.4 33.7 1.0
CG B:GLU249 4.5 51.5 1.0
O B:HOH733 4.5 33.4 1.0
OE1 B:GLU314 4.6 31.7 1.0
CZ B:ARG248 4.6 29.9 1.0
NE B:ARG248 4.9 28.1 1.0
CG2 B:VAL252 4.9 25.8 1.0
O B:ARG248 4.9 33.5 1.0

Reference:

X.W.Zou, Y.C.Liu, N.S.Hsu, C.J.Huang, S.Y.Lyu, H.C.Chan, C.Y.Chang, H.W.Yeh, K.H.Lin, C.J.Wu, M.D.Tsai, T.L.Li. Structure and Mechanism of A Nonhaem-Iron Sam-Dependent C-Methyltransferase and Its Engineering to A Hydratase and An O-Methyltransferase Acta Crystallogr.,Sect.D V. 70 1549 2014.
ISSN: ISSN 0907-4449
PubMed: 24914966
DOI: 10.1107/S1399004714005239
Page generated: Sun Jul 14 09:07:21 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy