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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

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Calcium binding site 1 out of 9 in the Crystal Structure of Methyltransferase From Streptomyces Hygroscopicus Complexed with 4-Hydroxyphenylpyruvic Acid


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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

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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

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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

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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

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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

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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

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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

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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

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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

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