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Magnesium in PDB 1jyl: Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc)

Protein crystallography data

The structure of Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc), PDB code: 1jyl was solved by B.-Y.Kwak, M.Yun, H.-W.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 48.200, 69.000, 81.600, 93.40, 92.80, 97.10
R / Rfree (%) 20.8 / 23.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc) (pdb code 1jyl). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc), PDB code: 1jyl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 1jyl

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Magnesium binding site 1 out of 4 in the Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1996

b:20.9
occ:1.00
OD2 A:ASP107 2.2 38.2 1.0
O2B A:CDC1991 2.4 11.0 1.0
OE2 A:GLU216 2.5 53.0 1.0
O2A A:CDC1991 2.5 14.9 1.0
OD1 A:ASP218 2.6 63.5 1.0
CG A:ASP107 2.9 36.5 1.0
CD A:GLU216 3.0 54.6 1.0
OD1 A:ASP107 3.1 38.3 1.0
OE1 A:GLU216 3.2 64.8 1.0
CG A:ASP218 3.4 68.4 1.0
OD2 A:ASP218 3.5 74.3 1.0
PB A:CDC1991 3.6 28.0 1.0
PA A:CDC1991 3.7 15.4 1.0
C5' A:CDC1991 3.8 21.2 1.0
O3A A:CDC1991 4.0 26.4 1.0
O5' A:CDC1991 4.1 24.3 1.0
O A:HOH5091 4.1 34.5 1.0
CG A:GLU216 4.2 49.4 1.0
CB A:ASP107 4.3 35.0 1.0
O1B A:CDC1991 4.3 35.9 1.0
NZ A:LYS28 4.4 21.7 1.0
O A:ASP107 4.8 28.4 1.0
CB A:ASP218 4.8 56.2 1.0
C14 A:CDC1991 4.8 36.3 1.0
O3B A:CDC1991 4.9 9.1 1.0
O1A A:CDC1991 5.0 33.3 1.0

Magnesium binding site 2 out of 4 in 1jyl

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Magnesium binding site 2 out of 4 in the Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg2996

b:20.6
occ:1.00
OD1 B:ASP107 2.3 23.7 1.0
O2B B:CDC2991 2.4 29.2 1.0
OD1 B:ASP218 2.4 36.3 1.0
O B:HOH5164 2.5 27.4 1.0
OE2 B:GLU216 2.5 35.5 1.0
O2A B:CDC2991 2.8 23.0 1.0
OD2 B:ASP107 2.8 23.2 1.0
CG B:ASP107 2.8 27.6 1.0
CD B:GLU216 3.2 30.6 1.0
CG B:ASP218 3.2 35.8 1.0
OD2 B:ASP218 3.4 23.4 1.0
PB B:CDC2991 3.6 27.4 1.0
NZ B:LYS28 3.8 23.9 1.0
CG B:GLU216 3.8 33.3 1.0
PA B:CDC2991 3.9 25.5 1.0
O B:HOH5153 3.9 18.4 1.0
OE1 B:GLU216 3.9 33.3 1.0
C5' B:CDC2991 3.9 29.8 1.0
O3A B:CDC2991 4.1 36.1 1.0
O5' B:CDC2991 4.2 24.4 1.0
CB B:ASP107 4.3 26.3 1.0
O1B B:CDC2991 4.3 26.8 1.0
CB B:ASP218 4.6 30.3 1.0
C14 B:CDC2991 4.8 29.2 1.0
O3B B:CDC2991 4.9 38.3 1.0
O B:ASP107 5.0 32.0 1.0
CA B:ASP218 5.0 32.9 1.0

Magnesium binding site 3 out of 4 in 1jyl

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Magnesium binding site 3 out of 4 in the Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg3996

b:31.3
occ:1.00
OD2 C:ASP107 2.1 30.1 1.0
O2B C:CDC3991 2.3 24.2 1.0
O2A C:CDC3991 2.6 17.2 1.0
OE2 C:GLU216 2.7 44.3 1.0
OD1 C:ASP218 2.7 66.1 1.0
CG C:ASP107 3.0 36.1 1.0
OD1 C:ASP107 3.3 33.5 1.0
CD C:GLU216 3.4 47.9 1.0
CG C:ASP218 3.5 62.4 1.0
PB C:CDC3991 3.5 33.4 1.0
OD2 C:ASP218 3.5 62.1 1.0
C5' C:CDC3991 3.6 38.0 1.0
PA C:CDC3991 3.7 22.4 1.0
O5' C:CDC3991 4.0 31.0 1.0
O C:HOH5131 4.0 24.8 1.0
O3A C:CDC3991 4.0 34.1 1.0
OE1 C:GLU216 4.0 55.2 1.0
O1B C:CDC3991 4.2 41.9 1.0
CG C:GLU216 4.2 44.7 1.0
NZ C:LYS28 4.2 38.8 1.0
CB C:ASP107 4.5 30.0 1.0
C14 C:CDC3991 4.7 40.6 1.0
O3B C:CDC3991 4.9 27.4 1.0
CB C:ASP218 4.9 54.7 1.0
C4' C:CDC3991 5.0 30.9 1.0

Magnesium binding site 4 out of 4 in 1jyl

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Magnesium binding site 4 out of 4 in the Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Catalytic Mechanism of Ctp:Phosphocholine Cytidylytransferase From Streptococcus Pneumoniae (Licc) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg4996

b:21.8
occ:1.00
OD1 D:ASP107 2.2 37.6 1.0
O2B D:CDC4991 2.4 26.0 1.0
OD2 D:ASP218 2.4 29.9 1.0
O D:HOH5165 2.6 26.8 1.0
OE1 D:GLU216 2.6 42.9 1.0
O2A D:CDC4991 2.9 13.4 1.0
CG D:ASP107 2.9 36.5 1.0
OD2 D:ASP107 3.0 33.2 1.0
CG D:ASP218 3.1 32.1 1.0
OD1 D:ASP218 3.2 24.3 1.0
CD D:GLU216 3.3 42.0 1.0
PB D:CDC4991 3.6 22.9 1.0
CG D:GLU216 3.7 41.1 1.0
PA D:CDC4991 3.8 15.6 1.0
NZ D:LYS28 3.9 34.4 1.0
O D:HOH5166 3.9 19.3 1.0
C5' D:CDC4991 3.9 27.6 1.0
O5' D:CDC4991 4.0 26.8 1.0
O3A D:CDC4991 4.1 31.3 1.0
OE2 D:GLU216 4.2 44.5 1.0
CB D:ASP107 4.3 33.9 1.0
O1B D:CDC4991 4.3 23.4 1.0
CB D:ASP218 4.6 30.3 1.0
C14 D:CDC4991 4.8 15.3 1.0
O3B D:CDC4991 4.9 24.9 1.0
O D:ILE217 5.0 30.2 1.0

Reference:

B.Y.Kwak, Y.M.Zhang, M.Yun, R.J.Heath, C.O.Rock, S.Jackowski, H.W.Park. Structure and Mechanism of Ctp:Phosphocholine Cytidylyltransferase (Licc) From Streptococcus Pneumoniae. J.Biol.Chem. V. 277 4343 2002.
ISSN: ISSN 0021-9258
PubMed: 11706035
DOI: 10.1074/JBC.M109163200
Page generated: Mon Dec 14 06:11:54 2020

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